Hi Guys, Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints. P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date. Thanks! Rui Error messages: Exception happened during processing of request from ('127.0.0.1'---------------------------------------- Exception happened during processing of request from (, 52259'127.0.0.1', 52260) Traceback (most recent call last): ) Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread ---------------------------------------- Exception happened during processing of request from (---------------------------------------- File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262---------------------------------------- ) Exception happened during processing of request from ('127.0.0.1'---------------------------------------- , ) Traceback (most recent call last): Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Exception happened during processing of request from 52261('127.0.0.1', ---------------------------------------- )Exception happened during processing of request from Traceback (most recent call last): 52263('127.0.0.1') File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Traceback (most recent call last): , 52265) File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) self.finish_request(request, client_address) self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" self.RequestHandlerClass(request, client_address, self) self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.RequestHandlerClass(request, client_address, self) self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.finish() self.RequestHandlerClass(request, client_address, self) self.finish() self.RequestHandlerClass(request, client_address, self) self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.finish() self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish self.wfile.flush() self.wfile.flush() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish self.wfile.flush() self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() self.finish() self.wfile.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe self._sock.sendall(view[write_offset:write_offset+buffer_size]) ---------------------------------------- self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe ---------------------------------------- self._sock.sendall(view[write_offset:write_offset+buffer_size]) ---------------------------------------- error: [Errno 32] Broken pipe ---------------------------------------- ---------------------------------------- error: [Errno 32] Broken pipe ----------------------------------------
Hi Rui, Are you using the upload tool available in the tool panel under 'Get Data'
'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Hi Sam, I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either. Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused. Here is the command I ran: 1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours: [image: Inline image 1] so the error message in step 4 above was: The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu. To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml ...migrate 7->8 ...migrate 8->9 from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command. vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this: vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Tool dependencies can be installed after the repositories have been installed as well. After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml. fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml I ran the command sh ./scripts/migrate_tools/0009_tools.sh and after that, the start up still shows some errors like: galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable. now if I do a 'grep IOError paster.log', I got the following: IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml' I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so. Could you please advise? Thanks, Rui On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com>wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data'
'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Hello Rui, the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution Please check the page and let us know if it helps you with your instance. Afterwards we can continue to troubleshoot the upload problems. goodluck Martin On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
[image: Inline image 1]
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com>wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Hi Martin, Thanks. I'll read the manual. Best, Rui On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
[image: Inline image 1]
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com>wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Rui, could you please try 'hg status' and tell us what it outputs? Thanks Martin On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
[image: Inline image 1]
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com>wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Hi Martin, Here you go. there are 493 files missing, seems. Thanks, Rui On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
[image: Inline image 1]
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com>wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution? thanks, Rui On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
[image: Inline image 1]
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com>wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
> Hi Guys, > > Our galaxy instance has been in use for a couple years but since Feb > 2014 it started to show us some weird behavior. Recently the upload > function suddenly stopped working properly. We are getting messages like > the following. I'm not sure if this only happens to us. If someone has seen > this before, please give me some hints. > > P.S., I searched online and many says that this is because the > browser does not wait till all the data from the server is received and > closes the socket. However it happens both in firefox and chrome. I'm > wondering if it is because galaxy has any change recently but when I do 'hg > update stable' it reported that it is up to date. > > Thanks! > Rui > > Error messages: > > Exception happened during processing of request from > ('127.0.0.1'---------------------------------------- > > Exception happened during processing of request from (, > 52259'127.0.0.1', 52260) > > Traceback (most recent call last): > > ) > > Traceback (most recent call last): > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > ---------------------------------------- > > Exception happened during processing of request from > (---------------------------------------- > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > Exception happened during processing of request from'127.0.0.1' , > ('127.0.0.1'52264, 52262---------------------------------------- > > ) > > Exception happened during processing of request from > ('127.0.0.1'---------------------------------------- > > , ) > > Traceback (most recent call last): > > Traceback (most recent call last): > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > Exception happened during processing of request from > 52261('127.0.0.1', ---------------------------------------- > > )Exception happened during processing of request from > > Traceback (most recent call last): > > 52263('127.0.0.1') > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > Traceback (most recent call last): > > , 52265) > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > Traceback (most recent call last): > > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", > line 1068, in process_request_in_thread > > self.finish_request(request, client_address) > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > self.finish_request(request, client_address) > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > self.finish_request(request, client_address) > > self.finish_request(request, client_address) > > self.finish_request(request, client_address) > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > self.finish_request(request, client_address) > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > self.finish_request(request, client_address) > > File "/usr/lib/python2.7/SocketServer.py", line 323, in > finish_request > > 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET > /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " > http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" > > self.RequestHandlerClass(request, client_address, self) > > self.RequestHandlerClass(request, client_address, self) > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > self.RequestHandlerClass(request, client_address, self) > > self.RequestHandlerClass(request, client_address, self) > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > self.finish() > > self.RequestHandlerClass(request, client_address, self) > > self.finish() > > self.RequestHandlerClass(request, client_address, self) > > self.finish() > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > self.RequestHandlerClass(request, client_address, self) > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ > > self.finish() > > self.finish() > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > self.wfile.flush() > > self.wfile.flush() > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > self.wfile.flush() > > self.finish() > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > self.wfile.flush() > > self.finish() > > self.wfile.flush() > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > self.wfile.flush() > > File "/usr/lib/python2.7/SocketServer.py", line 693, in finish > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > self.wfile.flush() > > File "/usr/lib/python2.7/socket.py", line 303, in flush > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > error: [Errno 32] Broken pipe > > error: [Errno 32] Broken pipe > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > ---------------------------------------- > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > error: [Errno 32] Broken pipe > > error: [Errno 32] Broken pipe > > error: [Errno 32] Broken pipe > > ---------------------------------------- > > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > > ---------------------------------------- > > error: [Errno 32] Broken pipe > > ---------------------------------------- > > ---------------------------------------- > > error: [Errno 32] Broken pipe > > ---------------------------------------- > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Question mark means 'untracked' so no problems there. Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again. M. On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
[image: Inline image 1]
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com > wrote:
> Hi Rui, > > Are you using the upload tool available in the tool panel under 'Get > Data' > 'Upload file from your computer'? Or the new upload dialog by > clicking on 'Load Data'? Could you also please let me know if this error > occurs always or just sometimes? > > Thanks Sam > > > On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: > >> Hi Guys, >> >> Our galaxy instance has been in use for a couple years but since >> Feb 2014 it started to show us some weird behavior. Recently the upload >> function suddenly stopped working properly. We are getting messages like >> the following. I'm not sure if this only happens to us. If someone has seen >> this before, please give me some hints. >> >> P.S., I searched online and many says that this is because the >> browser does not wait till all the data from the server is received and >> closes the socket. However it happens both in firefox and chrome. I'm >> wondering if it is because galaxy has any change recently but when I do 'hg >> update stable' it reported that it is up to date. >> >> Thanks! >> Rui >> >> Error messages: >> >> Exception happened during processing of request from >> ('127.0.0.1'---------------------------------------- >> >> Exception happened during processing of request from (, >> 52259'127.0.0.1', 52260) >> >> Traceback (most recent call last): >> >> ) >> >> Traceback (most recent call last): >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> ---------------------------------------- >> >> Exception happened during processing of request from >> (---------------------------------------- >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> Exception happened during processing of request from'127.0.0.1' , >> ('127.0.0.1'52264, 52262---------------------------------------- >> >> ) >> >> Exception happened during processing of request from >> ('127.0.0.1'---------------------------------------- >> >> , ) >> >> Traceback (most recent call last): >> >> Traceback (most recent call last): >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> Exception happened during processing of request from >> 52261('127.0.0.1', ---------------------------------------- >> >> )Exception happened during processing of request from >> >> Traceback (most recent call last): >> >> 52263('127.0.0.1') >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> Traceback (most recent call last): >> >> , 52265) >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> Traceback (most recent call last): >> >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >> line 1068, in process_request_in_thread >> >> self.finish_request(request, client_address) >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> self.finish_request(request, client_address) >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> self.finish_request(request, client_address) >> >> self.finish_request(request, client_address) >> >> self.finish_request(request, client_address) >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> self.finish_request(request, client_address) >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> self.finish_request(request, client_address) >> >> File "/usr/lib/python2.7/SocketServer.py", line 323, in >> finish_request >> >> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >> >> self.RequestHandlerClass(request, client_address, self) >> >> self.RequestHandlerClass(request, client_address, self) >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> self.RequestHandlerClass(request, client_address, self) >> >> self.RequestHandlerClass(request, client_address, self) >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> self.finish() >> >> self.RequestHandlerClass(request, client_address, self) >> >> self.finish() >> >> self.RequestHandlerClass(request, client_address, self) >> >> self.finish() >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> self.RequestHandlerClass(request, client_address, self) >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >> >> self.finish() >> >> self.finish() >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> self.wfile.flush() >> >> self.wfile.flush() >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> self.wfile.flush() >> >> self.finish() >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> self.wfile.flush() >> >> self.finish() >> >> self.wfile.flush() >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> self.wfile.flush() >> >> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> self.wfile.flush() >> >> File "/usr/lib/python2.7/socket.py", line 303, in flush >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> error: [Errno 32] Broken pipe >> >> error: [Errno 32] Broken pipe >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> ---------------------------------------- >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> error: [Errno 32] Broken pipe >> >> error: [Errno 32] Broken pipe >> >> error: [Errno 32] Broken pipe >> >> ---------------------------------------- >> >> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >> >> ---------------------------------------- >> >> error: [Errno 32] Broken pipe >> >> ---------------------------------------- >> >> ---------------------------------------- >> >> error: [Errno 32] Broken pipe >> >> ---------------------------------------- >> >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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I followed this instruction and the server started successfully. The whole thing starts with: python path is: /home/bioinfoadmin/app/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/lib, /usr/local/lib/python2.7/dist-packages/distribute-0.6.49-py2.7.egg, /usr/local/lib/python2.7/dist-packages/BETA_Package-0.1.5-py2.7.egg, /home/bioinfoadmin/app/dep/macs/1.4.2/lib/python2.7/site-packages, /home/bioinfoadmin/app/galaxy-dist, /usr/lib/python2.7, /usr/lib/python2.7/plat-linux2, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /usr/local/lib/python2.7/dist-packages, /usr/local/lib/python2.7/dist-packages/setuptools-0.6c11-py2.7.egg-info, /usr/lib/python2.7/dist-packages/PIL, /usr/lib/python2.7/dist-packages/gst-0.10, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/python2.7/dist-packages/ubuntu-sso-client, /usr/lib/python2.7/dist-packages/ubuntuone-client, /usr/lib/python2.7/dist-packages/ubuntuone-control-panel, /usr/lib/python2.7/dist-packages/ubuntuone-couch, /usr/lib/python2.7/dist-packages/ubuntuone-installer, /usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol, /usr/lib/python2.7/dist-packages tool_shed.tool_shed_registry DEBUG 2014-02-28 10:32:53,360 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2014-02-28 10:32:53,360 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2014-02-28 10:32:53,360 Loaded reference to tool shed: Galaxy test tool shed migrate.versioning.repository DEBUG 2014-02-28 10:32:53,427 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2014-02-28 10:32:53,428 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2014-02-28 10:32:53,428 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully Seems it did start the migration. The server started with a few errors like: galaxy.datatypes.registry DEBUG 2014-02-28 10:32:54,630 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,630 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'Eset' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'Eset' galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,631 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'CelZip' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'CelZip' galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,631 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'XysZip' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'XysZip' galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,631 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'Cel' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'Cel' I think this might be related to a customized tool. however, the history panel is still showing 'loading...' and tool panel is empty. same as the picture I sent last night. Thanks, Rui On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
> Hi Sam, > > I used Get Data and Upload file from your computer...and this just > started this Feb, actually a couple days ago it was fine. It happened > always, no matter we load from localhost or remote host, and other means > like paste the path etc didn't work either. > > Actually, I found that there are many released change on the galaxy > release and then I ran a 'hg pull -u'. However I had some error message > saying many of the tools installed are eliminated in the new distribution > and I could install them back from toolshed. I'm quite confused. > > Here is the command I ran: > > 1. hg pull -u > 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) > 3. sh manage_db.sh upgrade (update db to 118 version, start > again) > 4. ./run.sh --daemon (many error msg, I'll paste it below, but > next I did) > 5. sh ./scripts/migrate_tools/0009_tools.sh > > now after 5, I run it again, it started, but when I log in, seems > this page is hanging for few hours: > > [image: Inline image 1] > > so the error message in step 4 above was: > > The list of files at the end of this message refers to tools that > are configured to load into the tool panel for > this Galaxy instance, but have been removed from the Galaxy > distribution. These tools and their dependencies can be > automatically installed from the Galaxy tool shed at > http://toolshed.g2.bx.psu.edu. > > To skip this process, attempt to start your Galaxy server again > (e.g., sh run.sh or whatever you use). If you do this, > be aware that these tools will no longer be available in your Galaxy > tool panel, and entries for each of them should > be removed from your file named ./tool_conf.xml > > ...migrate 7->8 > ...migrate 8->9 > > from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu > and will be installed into your local Galaxy instance at the > location discussed above by running the following command. > > > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv > sh ./scripts/migrate_tools/0009_tools.sh > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > The tool dependencies listed above will be installed along with the > repositories if you add the 'install_dependencies' > option to the above command like this: > > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv > sh ./scripts/migrate_tools/0009_tools.sh install_dependencies > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > Tool dependencies can be installed after the repositories have been > installed as well. > > After the installation process finishes, you can start your Galaxy > server. As part of this installation process, > entries for each of the following tool config files will be added to > the file named ./migrated_tool_conf.xml, so these > tools will continue to be loaded into your tool panel. Because of > this, existing entries for these tools have been > removed from your file named ./tool_conf.xml. > > fastq_to_fasta.xml > execute_dwt_var_perFeature.xml > GMAJ.xml > rgWebLogo3.xml > rgClustalw.xml > gi2taxonomy.xml > t2t_report.xml > t2ps_wrapper.xml > find_diag_hits.xml > lca.xml > poisson2test.xml > rgFastQC.xml > fastq_groomer.xml > fastq_paired_end_splitter.xml > fastq_paired_end_joiner.xml > fastq_stats.xml > fastq_combiner.xml > fastq_filter.xml > fastq_trimmer.xml > fastq_trimmer_by_quality.xml > fastq_masker_by_quality.xml > fastq_paired_end_interlacer.xml > fastq_paired_end_deinterlacer.xml > fastq_manipulation.xml > fastq_to_tabular.xml > tabular_to_fastq.xml > bowtie2_wrapper.xml > tophat_wrapper.xml > tophat2_wrapper.xml > express_wrapper.xml > filter_transcripts_via_tracking.xml > macs_wrapper.xml > sicer_wrapper.xml > ccat_wrapper.xml > freebayes.xml > > I ran the command > > sh ./scripts/migrate_tools/0009_tools.sh > > and after that, the start up still shows some errors like: > > galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from > path: data_source/CR.xml > Traceback (most recent call last): > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 502, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), > guid=guid, repository_id=repository_id ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 615, in load_tool > tree = load_tool( config_file ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, > in load_tool > tree = parse_xml(path) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, > in parse_xml > tree = ElementTree.parse(fname) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 859, in parse > tree.parse(source, parser) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 576, in parse > source = open(source, "rb") > IOError: [Errno 2] No such file or directory: > './tools/data_source/CR.xml' > galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from > path: data_source/genomespace_file_browser_prod.xml > Traceback (most recent call last): > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 502, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), > guid=guid, repository_id=repository_id ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 615, in load_tool > tree = load_tool( config_file ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, > in load_tool > tree = parse_xml(path) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, > in parse_xml > tree = ElementTree.parse(fname) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 859, in parse > tree.parse(source, parser) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 576, in parse > source = open(source, "rb") > IOError: [Errno 2] No such file or directory: > './tools/data_source/genomespace_file_browser_prod.xml' > galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: > a when tag has been defined for 'genome_size_cond (genome_size) --> > 90300000', but does not appear to be selectable. > > now if I do a 'grep IOError paster.log', I got the following: > > IOError: [Errno 2] No such file or directory: > './tools/data_source/CR.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/genomespace_file_browser_prod.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/bx_browser.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/flymine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/flymine_test.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/modmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/mousemine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/ratmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/yeastmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/metabolicmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/encode_db.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/epigraph_import.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/epigraph_import_test.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_destination/epigraph.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_destination/epigraph_test.xml' > IOError: [Errno 2] No such file or directory: > './tools/encode/gencode_partition.xml' > IOError: [Errno 2] No such file or directory: > './tools/encode/random_intervals.xml' > IOError: [Errno 2] No such file or directory: > './tools/new_operations/column_join.xml' > IOError: [Errno 2] No such file or directory: > './tools/extract/phastOdds/phastOdds_tool.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/t_test_two_samples.xml' > IOError: [Errno 2] No such file or directory: > './tools/plotting/xy_plot.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/getIndels_3way.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/delete_overlapping_indels.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/compute_motifs_frequency.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/categorize_elements_satisfying_criteria.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/draw_stacked_barplots.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/microsatellite_birthdeath.xml' > IOError: [Errno 2] No such file or directory: > './tools/hyphy/hyphy_branch_lengths_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/hyphy/hyphy_nj_tree_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/hyphy/hyphy_dnds_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/evolution/mutate_snp_codon.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fasta_formatter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fasta_nucleotide_changer.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_collapser.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastq_quality_converter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_quality_statistics.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastq_quality_boxplot.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastq_quality_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_artifacts_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_barcode_splitter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_clipper.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_collapser.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_renamer.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_reverse_complement.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_trimmer.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/sam_indel_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/indel_sam2interval.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/indel_table.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/indel_analysis.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/tophat_color_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cufflinks_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cuffcompare_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cuffmerge_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cuffdiff_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_bitwise_flag_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam2interval.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_to_bam.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/bam_to_sam.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_merge.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_mpileup.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_pileup.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/pileup_parser.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/pileup_interval.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_flagstat.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_rmdup.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_slice_bam.xml' > IOError: [Errno 2] No such file or directory: > './tools/genetrack/genetrack_indexer.xml' > IOError: [Errno 2] No such file or directory: > './tools/genetrack/genetrack_peak_prediction.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgClean.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgPedSub.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgLDIndep.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgfakePhe.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgfakePed.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgQC.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgEigPCA.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgHaploView.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgManQQ.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgGRR.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgCaCo.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgTDT.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgGLM.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgManQQ.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/ctd.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/funDo.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/hilbertvis.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/dividePgSnpAlleles.xml' > IOError: [Errno 2] No such file or directory: > './tools/vcf_tools/intersect.xml' > > I'm not sure if I successfully updated galaxy source...since right > now the screen is always hanging. I think I miss some config files or so. > > Could you please advise? > > Thanks, > Rui > > > > > > > > > On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < > aysam.guerler@gmail.com> wrote: > >> Hi Rui, >> >> Are you using the upload tool available in the tool panel under >> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >> clicking on 'Load Data'? Could you also please let me know if this error >> occurs always or just sometimes? >> >> Thanks Sam >> >> >> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: >> >>> Hi Guys, >>> >>> Our galaxy instance has been in use for a couple years but since >>> Feb 2014 it started to show us some weird behavior. Recently the upload >>> function suddenly stopped working properly. We are getting messages like >>> the following. I'm not sure if this only happens to us. If someone has seen >>> this before, please give me some hints. >>> >>> P.S., I searched online and many says that this is because the >>> browser does not wait till all the data from the server is received and >>> closes the socket. However it happens both in firefox and chrome. I'm >>> wondering if it is because galaxy has any change recently but when I do 'hg >>> update stable' it reported that it is up to date. >>> >>> Thanks! >>> Rui >>> >>> Error messages: >>> >>> Exception happened during processing of request from >>> ('127.0.0.1'---------------------------------------- >>> >>> Exception happened during processing of request from (, >>> 52259'127.0.0.1', 52260) >>> >>> Traceback (most recent call last): >>> >>> ) >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> ---------------------------------------- >>> >>> Exception happened during processing of request from >>> (---------------------------------------- >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Exception happened during processing of request from'127.0.0.1' , >>> ('127.0.0.1'52264, 52262---------------------------------------- >>> >>> ) >>> >>> Exception happened during processing of request from >>> ('127.0.0.1'---------------------------------------- >>> >>> , ) >>> >>> Traceback (most recent call last): >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Exception happened during processing of request from >>> 52261('127.0.0.1', ---------------------------------------- >>> >>> )Exception happened during processing of request from >>> >>> Traceback (most recent call last): >>> >>> 52263('127.0.0.1') >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Traceback (most recent call last): >>> >>> , 52265) >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> self.finish_request(request, client_address) >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.finish() >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.finish() >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.finish() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.finish() >>> >>> self.finish() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> self.wfile.flush() >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> self.wfile.flush() >>> >>> self.finish() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self.wfile.flush() >>> >>> self.finish() >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> error: [Errno 32] Broken pipe >>> >>> error: [Errno 32] Broken pipe >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> ---------------------------------------- >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> error: [Errno 32] Broken pipe >>> >>> error: [Errno 32] Broken pipe >>> >>> error: [Errno 32] Broken pipe >>> >>> ---------------------------------------- >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> ---------------------------------------- >>> >>> error: [Errno 32] Broken pipe >>> >>> ---------------------------------------- >>> >>> ---------------------------------------- >>> >>> error: [Errno 32] Broken pipe >>> >>> ---------------------------------------- >>> >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
Hi Martin, So, after some effort, it started all ok now, and tool panel loaded. It was probably due to cistrome. However, when we upload file(using 'load data' or 'upload file from computer'), we have the following warning. After I make the dir to be 755, it worked. Seems I'm ready to go. Is this a right approach to solve it? Thanks, Rui /usr/local/lib/python2.7/dist-packages/distribute-0.6.49-py2.7.egg/pkg_resources.py:1025: UserWarning: /home/bioinfoadmin/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable). warnings.warn(msg, UserWarning) On Fri, Feb 28, 2014 at 10:41 AM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
I followed this instruction and the server started successfully. The whole thing starts with:
python path is: /home/bioinfoadmin/app/galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/amqplib-0.6.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/pexpect-2.4-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/WebHelpers-1.3-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Routes-1.12.3-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/wchartype-0.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/docutils-0.7-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg, /home/bioinfoadmin/app/galaxy-dist/lib, /usr/local/lib/python2.7/dist-packages/distribute-0.6.49-py2.7.egg, /usr/local/lib/python2.7/dist-packages/BETA_Package-0.1.5-py2.7.egg, /home/bioinfoadmin/app/dep/macs/1.4.2/lib/python2.7/site-packages, /home/bioinfoadmin/app/galaxy-dist, /usr/lib/python2.7, /usr/lib/python2.7/plat-linux2, /usr/lib/python2.7/lib-tk, /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload, /usr/local/lib/python2.7/dist-packages, /usr/local/lib/python2.7/dist-packages/setuptools-0.6c11-py2.7.egg-info, /usr/lib/python2.7/dist-packages/PIL, /usr/lib/python2.7/dist-packages/gst-0.10, /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/python2.7/dist-packages/ubuntu-sso-client, /usr/lib/python2.7/dist-packages/ubuntuone-client, /usr/lib/python2.7/dist-packages/ubuntuone-control-panel, /usr/lib/python2.7/dist-packages/ubuntuone-couch, /usr/lib/python2.7/dist-packages/ubuntuone-installer, /usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol, /usr/lib/python2.7/dist-packages tool_shed.tool_shed_registry DEBUG 2014-02-28 10:32:53,360 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2014-02-28 10:32:53,360 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2014-02-28 10:32:53,360 Loaded reference to tool shed: Galaxy test tool shed migrate.versioning.repository DEBUG 2014-02-28 10:32:53,427 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2014-02-28 10:32:53,428 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2014-02-28 10:32:53,428 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
Seems it did start the migration.
The server started with a few errors like:
galaxy.datatypes.registry DEBUG 2014-02-28 10:32:54,630 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,630 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'Eset' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'Eset' galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,631 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'CelZip' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'CelZip' galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,631 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'XysZip' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'XysZip' galaxy.datatypes.registry ERROR 2014-02-28 10:32:54,631 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'Cel' Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'Cel'
I think this might be related to a customized tool. however, the history panel is still showing 'loading...' and tool panel is empty. same as the picture I sent last night.
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote:
> Hello Rui, > > the process of migrating tools from Galaxy itself to the ToolShed > (Galaxy's appstore) is ongoing and is well described here: > https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution > > Please check the page and let us know if it helps you with your > instance. > > Afterwards we can continue to troubleshoot the upload problems. > > goodluck > > Martin > > > On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: > >> Hi Sam, >> >> I used Get Data and Upload file from your computer...and this just >> started this Feb, actually a couple days ago it was fine. It happened >> always, no matter we load from localhost or remote host, and other means >> like paste the path etc didn't work either. >> >> Actually, I found that there are many released change on the galaxy >> release and then I ran a 'hg pull -u'. However I had some error message >> saying many of the tools installed are eliminated in the new distribution >> and I could install them back from toolshed. I'm quite confused. >> >> Here is the command I ran: >> >> 1. hg pull -u >> 2. ./run.sh --daemon (many error msg, follow the suggestion,then >> ) >> 3. sh manage_db.sh upgrade (update db to 118 version, start >> again) >> 4. ./run.sh --daemon (many error msg, I'll paste it below, but >> next I did) >> 5. sh ./scripts/migrate_tools/0009_tools.sh >> >> now after 5, I run it again, it started, but when I log in, seems >> this page is hanging for few hours: >> >> [image: Inline image 1] >> >> so the error message in step 4 above was: >> >> The list of files at the end of this message refers to tools that >> are configured to load into the tool panel for >> this Galaxy instance, but have been removed from the Galaxy >> distribution. These tools and their dependencies can be >> automatically installed from the Galaxy tool shed at >> http://toolshed.g2.bx.psu.edu. >> >> To skip this process, attempt to start your Galaxy server again >> (e.g., sh run.sh or whatever you use). If you do this, >> be aware that these tools will no longer be available in your >> Galaxy tool panel, and entries for each of them should >> be removed from your file named ./tool_conf.xml >> >> ...migrate 7->8 >> ...migrate 8->9 >> >> from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu >> and will be installed into your local Galaxy instance at the >> location discussed above by running the following command. >> >> >> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >> sh ./scripts/migrate_tools/0009_tools.sh >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> The tool dependencies listed above will be installed along with the >> repositories if you add the 'install_dependencies' >> option to the above command like this: >> >> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >> sh ./scripts/migrate_tools/0009_tools.sh install_dependencies >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> Tool dependencies can be installed after the repositories have been >> installed as well. >> >> After the installation process finishes, you can start your Galaxy >> server. As part of this installation process, >> entries for each of the following tool config files will be added >> to the file named ./migrated_tool_conf.xml, so these >> tools will continue to be loaded into your tool panel. Because of >> this, existing entries for these tools have been >> removed from your file named ./tool_conf.xml. >> >> fastq_to_fasta.xml >> execute_dwt_var_perFeature.xml >> GMAJ.xml >> rgWebLogo3.xml >> rgClustalw.xml >> gi2taxonomy.xml >> t2t_report.xml >> t2ps_wrapper.xml >> find_diag_hits.xml >> lca.xml >> poisson2test.xml >> rgFastQC.xml >> fastq_groomer.xml >> fastq_paired_end_splitter.xml >> fastq_paired_end_joiner.xml >> fastq_stats.xml >> fastq_combiner.xml >> fastq_filter.xml >> fastq_trimmer.xml >> fastq_trimmer_by_quality.xml >> fastq_masker_by_quality.xml >> fastq_paired_end_interlacer.xml >> fastq_paired_end_deinterlacer.xml >> fastq_manipulation.xml >> fastq_to_tabular.xml >> tabular_to_fastq.xml >> bowtie2_wrapper.xml >> tophat_wrapper.xml >> tophat2_wrapper.xml >> express_wrapper.xml >> filter_transcripts_via_tracking.xml >> macs_wrapper.xml >> sicer_wrapper.xml >> ccat_wrapper.xml >> freebayes.xml >> >> I ran the command >> >> sh ./scripts/migrate_tools/0009_tools.sh >> >> and after that, the start up still shows some errors like: >> >> galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from >> path: data_source/CR.xml >> Traceback (most recent call last): >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 502, in load_tool_tag_set >> tool = self.load_tool( os.path.join( tool_path, path ), >> guid=guid, repository_id=repository_id ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 615, in load_tool >> tree = load_tool( config_file ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >> in load_tool >> tree = parse_xml(path) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >> in parse_xml >> tree = ElementTree.parse(fname) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 859, in parse >> tree.parse(source, parser) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 576, in parse >> source = open(source, "rb") >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/CR.xml' >> galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from >> path: data_source/genomespace_file_browser_prod.xml >> Traceback (most recent call last): >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 502, in load_tool_tag_set >> tool = self.load_tool( os.path.join( tool_path, path ), >> guid=guid, repository_id=repository_id ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 615, in load_tool >> tree = load_tool( config_file ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >> in load_tool >> tree = parse_xml(path) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >> in parse_xml >> tree = ElementTree.parse(fname) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 859, in parse >> tree.parse(source, parser) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 576, in parse >> source = open(source, "rb") >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/genomespace_file_browser_prod.xml' >> galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: >> a when tag has been defined for 'genome_size_cond (genome_size) --> >> 90300000', but does not appear to be selectable. >> >> now if I do a 'grep IOError paster.log', I got the following: >> >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/CR.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/genomespace_file_browser_prod.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/bx_browser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/flymine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/flymine_test.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/modmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/mousemine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/ratmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/yeastmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/metabolicmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/encode_db.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/epigraph_import.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/epigraph_import_test.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_destination/epigraph.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_destination/epigraph_test.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/encode/gencode_partition.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/encode/random_intervals.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/new_operations/column_join.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/extract/phastOdds/phastOdds_tool.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/t_test_two_samples.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/plotting/xy_plot.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/getIndels_3way.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/delete_overlapping_indels.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/compute_motifs_frequency.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/categorize_elements_satisfying_criteria.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/draw_stacked_barplots.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/microsatellite_birthdeath.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/hyphy/hyphy_branch_lengths_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/hyphy/hyphy_nj_tree_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/hyphy/hyphy_dnds_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/evolution/mutate_snp_codon.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fasta_formatter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fasta_nucleotide_changer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_collapser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastq_quality_converter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_quality_statistics.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastq_quality_boxplot.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastq_quality_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_artifacts_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_barcode_splitter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_clipper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_collapser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_renamer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_reverse_complement.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_trimmer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/sam_indel_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/indel_sam2interval.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/indel_table.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/indel_analysis.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/tophat_color_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cufflinks_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cuffcompare_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cuffmerge_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cuffdiff_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_bitwise_flag_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam2interval.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_to_bam.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/bam_to_sam.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_merge.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_mpileup.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_pileup.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/pileup_parser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/pileup_interval.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_flagstat.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_rmdup.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_slice_bam.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/genetrack/genetrack_indexer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/genetrack/genetrack_peak_prediction.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgClean.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgPedSub.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgLDIndep.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgfakePhe.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgfakePed.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgQC.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgEigPCA.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgHaploView.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgManQQ.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgGRR.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgCaCo.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgTDT.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgGLM.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgManQQ.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/ctd.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/funDo.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/hilbertvis.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/dividePgSnpAlleles.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/vcf_tools/intersect.xml' >> >> I'm not sure if I successfully updated galaxy source...since right >> now the screen is always hanging. I think I miss some config files or so. >> >> Could you please advise? >> >> Thanks, >> Rui >> >> >> >> >> >> >> >> >> On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < >> aysam.guerler@gmail.com> wrote: >> >>> Hi Rui, >>> >>> Are you using the upload tool available in the tool panel under >>> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >>> clicking on 'Load Data'? Could you also please let me know if this error >>> occurs always or just sometimes? >>> >>> Thanks Sam >>> >>> >>> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: >>> >>>> Hi Guys, >>>> >>>> Our galaxy instance has been in use for a couple years but since >>>> Feb 2014 it started to show us some weird behavior. Recently the upload >>>> function suddenly stopped working properly. We are getting messages like >>>> the following. I'm not sure if this only happens to us. If someone has seen >>>> this before, please give me some hints. >>>> >>>> P.S., I searched online and many says that this is because the >>>> browser does not wait till all the data from the server is received and >>>> closes the socket. However it happens both in firefox and chrome. I'm >>>> wondering if it is because galaxy has any change recently but when I do 'hg >>>> update stable' it reported that it is up to date. >>>> >>>> Thanks! >>>> Rui >>>> >>>> Error messages: >>>> >>>> Exception happened during processing of request from >>>> ('127.0.0.1'---------------------------------------- >>>> >>>> Exception happened during processing of request from (, >>>> 52259'127.0.0.1', 52260) >>>> >>>> Traceback (most recent call last): >>>> >>>> ) >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> ---------------------------------------- >>>> >>>> Exception happened during processing of request from >>>> (---------------------------------------- >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Exception happened during processing of request from'127.0.0.1' , >>>> ('127.0.0.1'52264, 52262---------------------------------------- >>>> >>>> ) >>>> >>>> Exception happened during processing of request from >>>> ('127.0.0.1'---------------------------------------- >>>> >>>> , ) >>>> >>>> Traceback (most recent call last): >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Exception happened during processing of request from >>>> 52261('127.0.0.1', ---------------------------------------- >>>> >>>> )Exception happened during processing of request from >>>> >>>> Traceback (most recent call last): >>>> >>>> 52263('127.0.0.1') >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Traceback (most recent call last): >>>> >>>> , 52265) >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> self.finish_request(request, client_address) >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.finish() >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.finish() >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.finish() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.finish() >>>> >>>> self.finish() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> self.wfile.flush() >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> self.wfile.flush() >>>> >>>> self.finish() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> self.wfile.flush() >>>> >>>> self.finish() >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> ---------------------------------------- >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> ---------------------------------------- >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> ---------------------------------------- >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> ---------------------------------------- >>>> >>>> ---------------------------------------- >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> ---------------------------------------- >>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >
Hi Martin, I'm seeing a lot of messages like: galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully and then tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories. I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script? Thanks, Rui On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
> Hi Sam, > > I used Get Data and Upload file from your computer...and this just > started this Feb, actually a couple days ago it was fine. It happened > always, no matter we load from localhost or remote host, and other means > like paste the path etc didn't work either. > > Actually, I found that there are many released change on the galaxy > release and then I ran a 'hg pull -u'. However I had some error message > saying many of the tools installed are eliminated in the new distribution > and I could install them back from toolshed. I'm quite confused. > > Here is the command I ran: > > 1. hg pull -u > 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) > 3. sh manage_db.sh upgrade (update db to 118 version, start > again) > 4. ./run.sh --daemon (many error msg, I'll paste it below, but > next I did) > 5. sh ./scripts/migrate_tools/0009_tools.sh > > now after 5, I run it again, it started, but when I log in, seems > this page is hanging for few hours: > > [image: Inline image 1] > > so the error message in step 4 above was: > > The list of files at the end of this message refers to tools that > are configured to load into the tool panel for > this Galaxy instance, but have been removed from the Galaxy > distribution. These tools and their dependencies can be > automatically installed from the Galaxy tool shed at > http://toolshed.g2.bx.psu.edu. > > To skip this process, attempt to start your Galaxy server again > (e.g., sh run.sh or whatever you use). If you do this, > be aware that these tools will no longer be available in your Galaxy > tool panel, and entries for each of them should > be removed from your file named ./tool_conf.xml > > ...migrate 7->8 > ...migrate 8->9 > > from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu > and will be installed into your local Galaxy instance at the > location discussed above by running the following command. > > > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv > sh ./scripts/migrate_tools/0009_tools.sh > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > The tool dependencies listed above will be installed along with the > repositories if you add the 'install_dependencies' > option to the above command like this: > > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv > sh ./scripts/migrate_tools/0009_tools.sh install_dependencies > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > Tool dependencies can be installed after the repositories have been > installed as well. > > After the installation process finishes, you can start your Galaxy > server. As part of this installation process, > entries for each of the following tool config files will be added to > the file named ./migrated_tool_conf.xml, so these > tools will continue to be loaded into your tool panel. Because of > this, existing entries for these tools have been > removed from your file named ./tool_conf.xml. > > fastq_to_fasta.xml > execute_dwt_var_perFeature.xml > GMAJ.xml > rgWebLogo3.xml > rgClustalw.xml > gi2taxonomy.xml > t2t_report.xml > t2ps_wrapper.xml > find_diag_hits.xml > lca.xml > poisson2test.xml > rgFastQC.xml > fastq_groomer.xml > fastq_paired_end_splitter.xml > fastq_paired_end_joiner.xml > fastq_stats.xml > fastq_combiner.xml > fastq_filter.xml > fastq_trimmer.xml > fastq_trimmer_by_quality.xml > fastq_masker_by_quality.xml > fastq_paired_end_interlacer.xml > fastq_paired_end_deinterlacer.xml > fastq_manipulation.xml > fastq_to_tabular.xml > tabular_to_fastq.xml > bowtie2_wrapper.xml > tophat_wrapper.xml > tophat2_wrapper.xml > express_wrapper.xml > filter_transcripts_via_tracking.xml > macs_wrapper.xml > sicer_wrapper.xml > ccat_wrapper.xml > freebayes.xml > > I ran the command > > sh ./scripts/migrate_tools/0009_tools.sh > > and after that, the start up still shows some errors like: > > galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from > path: data_source/CR.xml > Traceback (most recent call last): > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 502, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), > guid=guid, repository_id=repository_id ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 615, in load_tool > tree = load_tool( config_file ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, > in load_tool > tree = parse_xml(path) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, > in parse_xml > tree = ElementTree.parse(fname) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 859, in parse > tree.parse(source, parser) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 576, in parse > source = open(source, "rb") > IOError: [Errno 2] No such file or directory: > './tools/data_source/CR.xml' > galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from > path: data_source/genomespace_file_browser_prod.xml > Traceback (most recent call last): > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 502, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), > guid=guid, repository_id=repository_id ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line > 615, in load_tool > tree = load_tool( config_file ) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, > in load_tool > tree = parse_xml(path) > File > "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, > in parse_xml > tree = ElementTree.parse(fname) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 859, in parse > tree.parse(source, parser) > File > "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", > line 576, in parse > source = open(source, "rb") > IOError: [Errno 2] No such file or directory: > './tools/data_source/genomespace_file_browser_prod.xml' > galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: > a when tag has been defined for 'genome_size_cond (genome_size) --> > 90300000', but does not appear to be selectable. > > now if I do a 'grep IOError paster.log', I got the following: > > IOError: [Errno 2] No such file or directory: > './tools/data_source/CR.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/genomespace_file_browser_prod.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/bx_browser.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/flymine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/flymine_test.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/modmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/mousemine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/ratmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/yeastmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/metabolicmine.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/encode_db.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/epigraph_import.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_source/epigraph_import_test.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_destination/epigraph.xml' > IOError: [Errno 2] No such file or directory: > './tools/data_destination/epigraph_test.xml' > IOError: [Errno 2] No such file or directory: > './tools/encode/gencode_partition.xml' > IOError: [Errno 2] No such file or directory: > './tools/encode/random_intervals.xml' > IOError: [Errno 2] No such file or directory: > './tools/new_operations/column_join.xml' > IOError: [Errno 2] No such file or directory: > './tools/extract/phastOdds/phastOdds_tool.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/t_test_two_samples.xml' > IOError: [Errno 2] No such file or directory: > './tools/plotting/xy_plot.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/getIndels_3way.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/delete_overlapping_indels.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/compute_motifs_frequency.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/categorize_elements_satisfying_criteria.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/draw_stacked_barplots.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' > IOError: [Errno 2] No such file or directory: > './tools/regVariation/microsatellite_birthdeath.xml' > IOError: [Errno 2] No such file or directory: > './tools/hyphy/hyphy_branch_lengths_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/hyphy/hyphy_nj_tree_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/hyphy/hyphy_dnds_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/evolution/mutate_snp_codon.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fasta_formatter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fasta_nucleotide_changer.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_collapser.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastq_quality_converter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_quality_statistics.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastq_quality_boxplot.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastq_quality_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_artifacts_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_barcode_splitter.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_clipper.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_collapser.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_renamer.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_reverse_complement.xml' > IOError: [Errno 2] No such file or directory: > './tools/fastx_toolkit/fastx_trimmer.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/sam_indel_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/indel_sam2interval.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/indel_table.xml' > IOError: [Errno 2] No such file or directory: > './tools/indels/indel_analysis.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/tophat_color_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cufflinks_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cuffcompare_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cuffmerge_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/ngs_rna/cuffdiff_wrapper.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_bitwise_flag_filter.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam2interval.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_to_bam.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/bam_to_sam.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_merge.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_mpileup.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/sam_pileup.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/pileup_parser.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/pileup_interval.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_flagstat.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_rmdup.xml' > IOError: [Errno 2] No such file or directory: > './tools/samtools/samtools_slice_bam.xml' > IOError: [Errno 2] No such file or directory: > './tools/genetrack/genetrack_indexer.xml' > IOError: [Errno 2] No such file or directory: > './tools/genetrack/genetrack_peak_prediction.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgClean.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgPedSub.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgLDIndep.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgfakePhe.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgfakePed.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgQC.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgEigPCA.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgHaploView.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgManQQ.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgGRR.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgCaCo.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgTDT.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgGLM.xml' > IOError: [Errno 2] No such file or directory: > './tools/rgenetics/rgManQQ.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/ctd.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/funDo.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/hilbertvis.xml' > IOError: [Errno 2] No such file or directory: > './tools/phenotype_association/dividePgSnpAlleles.xml' > IOError: [Errno 2] No such file or directory: > './tools/vcf_tools/intersect.xml' > > I'm not sure if I successfully updated galaxy source...since right > now the screen is always hanging. I think I miss some config files or so. > > Could you please advise? > > Thanks, > Rui > > > > > > > > > On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < > aysam.guerler@gmail.com> wrote: > >> Hi Rui, >> >> Are you using the upload tool available in the tool panel under >> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >> clicking on 'Load Data'? Could you also please let me know if this error >> occurs always or just sometimes? >> >> Thanks Sam >> >> >> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: >> >>> Hi Guys, >>> >>> Our galaxy instance has been in use for a couple years but since >>> Feb 2014 it started to show us some weird behavior. Recently the upload >>> function suddenly stopped working properly. We are getting messages like >>> the following. I'm not sure if this only happens to us. If someone has seen >>> this before, please give me some hints. >>> >>> P.S., I searched online and many says that this is because the >>> browser does not wait till all the data from the server is received and >>> closes the socket. However it happens both in firefox and chrome. I'm >>> wondering if it is because galaxy has any change recently but when I do 'hg >>> update stable' it reported that it is up to date. >>> >>> Thanks! >>> Rui >>> >>> Error messages: >>> >>> Exception happened during processing of request from >>> ('127.0.0.1'---------------------------------------- >>> >>> Exception happened during processing of request from (, >>> 52259'127.0.0.1', 52260) >>> >>> Traceback (most recent call last): >>> >>> ) >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> ---------------------------------------- >>> >>> Exception happened during processing of request from >>> (---------------------------------------- >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Exception happened during processing of request from'127.0.0.1' , >>> ('127.0.0.1'52264, 52262---------------------------------------- >>> >>> ) >>> >>> Exception happened during processing of request from >>> ('127.0.0.1'---------------------------------------- >>> >>> , ) >>> >>> Traceback (most recent call last): >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Exception happened during processing of request from >>> 52261('127.0.0.1', ---------------------------------------- >>> >>> )Exception happened during processing of request from >>> >>> Traceback (most recent call last): >>> >>> 52263('127.0.0.1') >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Traceback (most recent call last): >>> >>> , 52265) >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> Traceback (most recent call last): >>> >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>> line 1068, in process_request_in_thread >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> self.finish_request(request, client_address) >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> self.finish_request(request, client_address) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>> finish_request >>> >>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.finish() >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.finish() >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> self.finish() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.RequestHandlerClass(request, client_address, self) >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>> >>> self.finish() >>> >>> self.finish() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> self.wfile.flush() >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> self.wfile.flush() >>> >>> self.finish() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self.wfile.flush() >>> >>> self.finish() >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self.wfile.flush() >>> >>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> error: [Errno 32] Broken pipe >>> >>> error: [Errno 32] Broken pipe >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> ---------------------------------------- >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> error: [Errno 32] Broken pipe >>> >>> error: [Errno 32] Broken pipe >>> >>> error: [Errno 32] Broken pipe >>> >>> ---------------------------------------- >>> >>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>> >>> ---------------------------------------- >>> >>> error: [Errno 32] Broken pipe >>> >>> ---------------------------------------- >>> >>> ---------------------------------------- >>> >>> error: [Errno 32] Broken pipe >>> >>> ---------------------------------------- >>> >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
Rui, it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly. M. On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote:
> Hello Rui, > > the process of migrating tools from Galaxy itself to the ToolShed > (Galaxy's appstore) is ongoing and is well described here: > https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution > > Please check the page and let us know if it helps you with your > instance. > > Afterwards we can continue to troubleshoot the upload problems. > > goodluck > > Martin > > > On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: > >> Hi Sam, >> >> I used Get Data and Upload file from your computer...and this just >> started this Feb, actually a couple days ago it was fine. It happened >> always, no matter we load from localhost or remote host, and other means >> like paste the path etc didn't work either. >> >> Actually, I found that there are many released change on the galaxy >> release and then I ran a 'hg pull -u'. However I had some error message >> saying many of the tools installed are eliminated in the new distribution >> and I could install them back from toolshed. I'm quite confused. >> >> Here is the command I ran: >> >> 1. hg pull -u >> 2. ./run.sh --daemon (many error msg, follow the suggestion,then >> ) >> 3. sh manage_db.sh upgrade (update db to 118 version, start >> again) >> 4. ./run.sh --daemon (many error msg, I'll paste it below, but >> next I did) >> 5. sh ./scripts/migrate_tools/0009_tools.sh >> >> now after 5, I run it again, it started, but when I log in, seems >> this page is hanging for few hours: >> >> [image: Inline image 1] >> >> so the error message in step 4 above was: >> >> The list of files at the end of this message refers to tools that >> are configured to load into the tool panel for >> this Galaxy instance, but have been removed from the Galaxy >> distribution. These tools and their dependencies can be >> automatically installed from the Galaxy tool shed at >> http://toolshed.g2.bx.psu.edu. >> >> To skip this process, attempt to start your Galaxy server again >> (e.g., sh run.sh or whatever you use). If you do this, >> be aware that these tools will no longer be available in your >> Galaxy tool panel, and entries for each of them should >> be removed from your file named ./tool_conf.xml >> >> ...migrate 7->8 >> ...migrate 8->9 >> >> from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu >> and will be installed into your local Galaxy instance at the >> location discussed above by running the following command. >> >> >> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >> sh ./scripts/migrate_tools/0009_tools.sh >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> The tool dependencies listed above will be installed along with the >> repositories if you add the 'install_dependencies' >> option to the above command like this: >> >> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >> sh ./scripts/migrate_tools/0009_tools.sh install_dependencies >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> Tool dependencies can be installed after the repositories have been >> installed as well. >> >> After the installation process finishes, you can start your Galaxy >> server. As part of this installation process, >> entries for each of the following tool config files will be added >> to the file named ./migrated_tool_conf.xml, so these >> tools will continue to be loaded into your tool panel. Because of >> this, existing entries for these tools have been >> removed from your file named ./tool_conf.xml. >> >> fastq_to_fasta.xml >> execute_dwt_var_perFeature.xml >> GMAJ.xml >> rgWebLogo3.xml >> rgClustalw.xml >> gi2taxonomy.xml >> t2t_report.xml >> t2ps_wrapper.xml >> find_diag_hits.xml >> lca.xml >> poisson2test.xml >> rgFastQC.xml >> fastq_groomer.xml >> fastq_paired_end_splitter.xml >> fastq_paired_end_joiner.xml >> fastq_stats.xml >> fastq_combiner.xml >> fastq_filter.xml >> fastq_trimmer.xml >> fastq_trimmer_by_quality.xml >> fastq_masker_by_quality.xml >> fastq_paired_end_interlacer.xml >> fastq_paired_end_deinterlacer.xml >> fastq_manipulation.xml >> fastq_to_tabular.xml >> tabular_to_fastq.xml >> bowtie2_wrapper.xml >> tophat_wrapper.xml >> tophat2_wrapper.xml >> express_wrapper.xml >> filter_transcripts_via_tracking.xml >> macs_wrapper.xml >> sicer_wrapper.xml >> ccat_wrapper.xml >> freebayes.xml >> >> I ran the command >> >> sh ./scripts/migrate_tools/0009_tools.sh >> >> and after that, the start up still shows some errors like: >> >> galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from >> path: data_source/CR.xml >> Traceback (most recent call last): >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 502, in load_tool_tag_set >> tool = self.load_tool( os.path.join( tool_path, path ), >> guid=guid, repository_id=repository_id ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 615, in load_tool >> tree = load_tool( config_file ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >> in load_tool >> tree = parse_xml(path) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >> in parse_xml >> tree = ElementTree.parse(fname) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 859, in parse >> tree.parse(source, parser) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 576, in parse >> source = open(source, "rb") >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/CR.xml' >> galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from >> path: data_source/genomespace_file_browser_prod.xml >> Traceback (most recent call last): >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 502, in load_tool_tag_set >> tool = self.load_tool( os.path.join( tool_path, path ), >> guid=guid, repository_id=repository_id ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >> 615, in load_tool >> tree = load_tool( config_file ) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >> in load_tool >> tree = parse_xml(path) >> File >> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >> in parse_xml >> tree = ElementTree.parse(fname) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 859, in parse >> tree.parse(source, parser) >> File >> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >> line 576, in parse >> source = open(source, "rb") >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/genomespace_file_browser_prod.xml' >> galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: >> a when tag has been defined for 'genome_size_cond (genome_size) --> >> 90300000', but does not appear to be selectable. >> >> now if I do a 'grep IOError paster.log', I got the following: >> >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/CR.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/genomespace_file_browser_prod.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/bx_browser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/flymine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/flymine_test.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/modmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/mousemine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/ratmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/yeastmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/metabolicmine.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/encode_db.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/epigraph_import.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_source/epigraph_import_test.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_destination/epigraph.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/data_destination/epigraph_test.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/encode/gencode_partition.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/encode/random_intervals.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/new_operations/column_join.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/extract/phastOdds/phastOdds_tool.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/t_test_two_samples.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/plotting/xy_plot.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/getIndels_3way.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/delete_overlapping_indels.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/compute_motifs_frequency.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/categorize_elements_satisfying_criteria.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/draw_stacked_barplots.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/regVariation/microsatellite_birthdeath.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/hyphy/hyphy_branch_lengths_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/hyphy/hyphy_nj_tree_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/hyphy/hyphy_dnds_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/evolution/mutate_snp_codon.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fasta_formatter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fasta_nucleotide_changer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_collapser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastq_quality_converter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_quality_statistics.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastq_quality_boxplot.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastq_quality_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_artifacts_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_barcode_splitter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_clipper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_collapser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_renamer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_reverse_complement.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/fastx_toolkit/fastx_trimmer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/sam_indel_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/indel_sam2interval.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/indel_table.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/indels/indel_analysis.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/tophat_color_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cufflinks_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cuffcompare_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cuffmerge_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/ngs_rna/cuffdiff_wrapper.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_bitwise_flag_filter.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam2interval.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_to_bam.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/bam_to_sam.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_merge.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_mpileup.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/sam_pileup.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/pileup_parser.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/pileup_interval.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_flagstat.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_rmdup.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/samtools/samtools_slice_bam.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/genetrack/genetrack_indexer.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/genetrack/genetrack_peak_prediction.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgClean.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgPedSub.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgLDIndep.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgfakePhe.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgfakePed.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgQC.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgEigPCA.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgHaploView.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgManQQ.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgGRR.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgCaCo.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgTDT.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgGLM.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/rgenetics/rgManQQ.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/ctd.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/funDo.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/hilbertvis.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/phenotype_association/dividePgSnpAlleles.xml' >> IOError: [Errno 2] No such file or directory: >> './tools/vcf_tools/intersect.xml' >> >> I'm not sure if I successfully updated galaxy source...since right >> now the screen is always hanging. I think I miss some config files or so. >> >> Could you please advise? >> >> Thanks, >> Rui >> >> >> >> >> >> >> >> >> On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < >> aysam.guerler@gmail.com> wrote: >> >>> Hi Rui, >>> >>> Are you using the upload tool available in the tool panel under >>> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >>> clicking on 'Load Data'? Could you also please let me know if this error >>> occurs always or just sometimes? >>> >>> Thanks Sam >>> >>> >>> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: >>> >>>> Hi Guys, >>>> >>>> Our galaxy instance has been in use for a couple years but since >>>> Feb 2014 it started to show us some weird behavior. Recently the upload >>>> function suddenly stopped working properly. We are getting messages like >>>> the following. I'm not sure if this only happens to us. If someone has seen >>>> this before, please give me some hints. >>>> >>>> P.S., I searched online and many says that this is because the >>>> browser does not wait till all the data from the server is received and >>>> closes the socket. However it happens both in firefox and chrome. I'm >>>> wondering if it is because galaxy has any change recently but when I do 'hg >>>> update stable' it reported that it is up to date. >>>> >>>> Thanks! >>>> Rui >>>> >>>> Error messages: >>>> >>>> Exception happened during processing of request from >>>> ('127.0.0.1'---------------------------------------- >>>> >>>> Exception happened during processing of request from (, >>>> 52259'127.0.0.1', 52260) >>>> >>>> Traceback (most recent call last): >>>> >>>> ) >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> ---------------------------------------- >>>> >>>> Exception happened during processing of request from >>>> (---------------------------------------- >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Exception happened during processing of request from'127.0.0.1' , >>>> ('127.0.0.1'52264, 52262---------------------------------------- >>>> >>>> ) >>>> >>>> Exception happened during processing of request from >>>> ('127.0.0.1'---------------------------------------- >>>> >>>> , ) >>>> >>>> Traceback (most recent call last): >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Exception happened during processing of request from >>>> 52261('127.0.0.1', ---------------------------------------- >>>> >>>> )Exception happened during processing of request from >>>> >>>> Traceback (most recent call last): >>>> >>>> 52263('127.0.0.1') >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Traceback (most recent call last): >>>> >>>> , 52265) >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> Traceback (most recent call last): >>>> >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>> line 1068, in process_request_in_thread >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> self.finish_request(request, client_address) >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> self.finish_request(request, client_address) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>> finish_request >>>> >>>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.finish() >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.finish() >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> self.finish() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.RequestHandlerClass(request, client_address, self) >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ >>>> >>>> self.finish() >>>> >>>> self.finish() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> self.wfile.flush() >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> self.wfile.flush() >>>> >>>> self.finish() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> self.wfile.flush() >>>> >>>> self.finish() >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> self.wfile.flush() >>>> >>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> ---------------------------------------- >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> ---------------------------------------- >>>> >>>> >>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>> >>>> ---------------------------------------- >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> ---------------------------------------- >>>> >>>> ---------------------------------------- >>>> >>>> error: [Errno 32] Broken pipe >>>> >>>> ---------------------------------------- >>>> >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >
Hi Martin, So, after some effort, things seem to be working. Thanks for the help along the way. However, one more error happened. Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well. Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml: <section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file=" toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>ae2ec275332a</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 </id> <version>1.0.1</version> </tool> </section> if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml, we could see that in this dir /home/bioinfoadmin/app/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs, there is a tool_dependency xml file that has following content: <?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed=" http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice? while in the same dir, macs_wrapper.xml has: <requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements> Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error. So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess? I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version? Thanks, Rui On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu>wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
> Hi Martin, > > Thanks. I'll read the manual. > > Best, > Rui > > > On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote: > >> Hello Rui, >> >> the process of migrating tools from Galaxy itself to the ToolShed >> (Galaxy's appstore) is ongoing and is well described here: >> https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution >> >> Please check the page and let us know if it helps you with your >> instance. >> >> Afterwards we can continue to troubleshoot the upload problems. >> >> goodluck >> >> Martin >> >> >> On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: >> >>> Hi Sam, >>> >>> I used Get Data and Upload file from your computer...and this just >>> started this Feb, actually a couple days ago it was fine. It happened >>> always, no matter we load from localhost or remote host, and other means >>> like paste the path etc didn't work either. >>> >>> Actually, I found that there are many released change on the >>> galaxy release and then I ran a 'hg pull -u'. However I had some error >>> message saying many of the tools installed are eliminated in the new >>> distribution and I could install them back from toolshed. I'm quite >>> confused. >>> >>> Here is the command I ran: >>> >>> 1. hg pull -u >>> 2. ./run.sh --daemon (many error msg, follow the >>> suggestion,then ) >>> 3. sh manage_db.sh upgrade (update db to 118 version, start >>> again) >>> 4. ./run.sh --daemon (many error msg, I'll paste it below, but >>> next I did) >>> 5. sh ./scripts/migrate_tools/0009_tools.sh >>> >>> now after 5, I run it again, it started, but when I log in, seems >>> this page is hanging for few hours: >>> >>> [image: Inline image 1] >>> >>> so the error message in step 4 above was: >>> >>> The list of files at the end of this message refers to tools that >>> are configured to load into the tool panel for >>> this Galaxy instance, but have been removed from the Galaxy >>> distribution. These tools and their dependencies can be >>> automatically installed from the Galaxy tool shed at >>> http://toolshed.g2.bx.psu.edu. >>> >>> To skip this process, attempt to start your Galaxy server again >>> (e.g., sh run.sh or whatever you use). If you do this, >>> be aware that these tools will no longer be available in your >>> Galaxy tool panel, and entries for each of them should >>> be removed from your file named ./tool_conf.xml >>> >>> ...migrate 7->8 >>> ...migrate 8->9 >>> >>> from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu >>> and will be installed into your local Galaxy instance at the >>> location discussed above by running the following command. >>> >>> >>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>> sh ./scripts/migrate_tools/0009_tools.sh >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> >>> The tool dependencies listed above will be installed along with >>> the repositories if you add the 'install_dependencies' >>> option to the above command like this: >>> >>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>> sh ./scripts/migrate_tools/0009_tools.sh install_dependencies >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> >>> Tool dependencies can be installed after the repositories have >>> been installed as well. >>> >>> After the installation process finishes, you can start your Galaxy >>> server. As part of this installation process, >>> entries for each of the following tool config files will be added >>> to the file named ./migrated_tool_conf.xml, so these >>> tools will continue to be loaded into your tool panel. Because of >>> this, existing entries for these tools have been >>> removed from your file named ./tool_conf.xml. >>> >>> fastq_to_fasta.xml >>> execute_dwt_var_perFeature.xml >>> GMAJ.xml >>> rgWebLogo3.xml >>> rgClustalw.xml >>> gi2taxonomy.xml >>> t2t_report.xml >>> t2ps_wrapper.xml >>> find_diag_hits.xml >>> lca.xml >>> poisson2test.xml >>> rgFastQC.xml >>> fastq_groomer.xml >>> fastq_paired_end_splitter.xml >>> fastq_paired_end_joiner.xml >>> fastq_stats.xml >>> fastq_combiner.xml >>> fastq_filter.xml >>> fastq_trimmer.xml >>> fastq_trimmer_by_quality.xml >>> fastq_masker_by_quality.xml >>> fastq_paired_end_interlacer.xml >>> fastq_paired_end_deinterlacer.xml >>> fastq_manipulation.xml >>> fastq_to_tabular.xml >>> tabular_to_fastq.xml >>> bowtie2_wrapper.xml >>> tophat_wrapper.xml >>> tophat2_wrapper.xml >>> express_wrapper.xml >>> filter_transcripts_via_tracking.xml >>> macs_wrapper.xml >>> sicer_wrapper.xml >>> ccat_wrapper.xml >>> freebayes.xml >>> >>> I ran the command >>> >>> sh ./scripts/migrate_tools/0009_tools.sh >>> >>> and after that, the start up still shows some errors like: >>> >>> galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from >>> path: data_source/CR.xml >>> Traceback (most recent call last): >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>> 502, in load_tool_tag_set >>> tool = self.load_tool( os.path.join( tool_path, path ), >>> guid=guid, repository_id=repository_id ) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>> 615, in load_tool >>> tree = load_tool( config_file ) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>> in load_tool >>> tree = parse_xml(path) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>> in parse_xml >>> tree = ElementTree.parse(fname) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>> line 859, in parse >>> tree.parse(source, parser) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>> line 576, in parse >>> source = open(source, "rb") >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/CR.xml' >>> galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from >>> path: data_source/genomespace_file_browser_prod.xml >>> Traceback (most recent call last): >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>> 502, in load_tool_tag_set >>> tool = self.load_tool( os.path.join( tool_path, path ), >>> guid=guid, repository_id=repository_id ) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>> 615, in load_tool >>> tree = load_tool( config_file ) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>> in load_tool >>> tree = parse_xml(path) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>> in parse_xml >>> tree = ElementTree.parse(fname) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>> line 859, in parse >>> tree.parse(source, parser) >>> File >>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>> line 576, in parse >>> source = open(source, "rb") >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/genomespace_file_browser_prod.xml' >>> galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool >>> peakcalling_macs: a when tag has been defined for 'genome_size_cond >>> (genome_size) --> 90300000', but does not appear to be selectable. >>> >>> now if I do a 'grep IOError paster.log', I got the following: >>> >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/CR.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/genomespace_file_browser_prod.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/bx_browser.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/flymine.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/flymine_test.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/modmine.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/mousemine.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/ratmine.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/yeastmine.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/metabolicmine.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/encode_db.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/epigraph_import.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_source/epigraph_import_test.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_destination/epigraph.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/data_destination/epigraph_test.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/encode/gencode_partition.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/encode/random_intervals.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/new_operations/column_join.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/extract/phastOdds/phastOdds_tool.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/t_test_two_samples.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/plotting/xy_plot.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/getIndels_3way.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/delete_overlapping_indels.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/compute_motifs_frequency.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/categorize_elements_satisfying_criteria.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/draw_stacked_barplots.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/regVariation/microsatellite_birthdeath.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/hyphy/hyphy_branch_lengths_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/hyphy/hyphy_nj_tree_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/hyphy/hyphy_dnds_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/evolution/mutate_snp_codon.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fasta_formatter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fasta_nucleotide_changer.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_collapser.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastq_quality_converter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_quality_statistics.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastq_quality_boxplot.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastq_quality_filter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_artifacts_filter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_barcode_splitter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_clipper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_collapser.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_renamer.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_reverse_complement.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/fastx_toolkit/fastx_trimmer.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/indels/sam_indel_filter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/indels/indel_sam2interval.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/indels/indel_table.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/indels/indel_analysis.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/ngs_rna/tophat_color_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/ngs_rna/cufflinks_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/ngs_rna/cuffcompare_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/ngs_rna/cuffmerge_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/ngs_rna/cuffdiff_wrapper.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/sam_bitwise_flag_filter.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/sam2interval.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/sam_to_bam.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/bam_to_sam.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/sam_merge.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/samtools_mpileup.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/sam_pileup.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/pileup_parser.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/pileup_interval.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/samtools_flagstat.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/samtools_rmdup.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/samtools/samtools_slice_bam.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/genetrack/genetrack_indexer.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/genetrack/genetrack_peak_prediction.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgClean.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgPedSub.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgLDIndep.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgfakePhe.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgfakePed.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgQC.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgEigPCA.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgHaploView.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgManQQ.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgGRR.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgCaCo.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgTDT.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgGLM.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/rgenetics/rgManQQ.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/phenotype_association/ctd.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/phenotype_association/funDo.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/phenotype_association/hilbertvis.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/phenotype_association/dividePgSnpAlleles.xml' >>> IOError: [Errno 2] No such file or directory: >>> './tools/vcf_tools/intersect.xml' >>> >>> I'm not sure if I successfully updated galaxy source...since right >>> now the screen is always hanging. I think I miss some config files or so. >>> >>> Could you please advise? >>> >>> Thanks, >>> Rui >>> >>> >>> >>> >>> >>> >>> >>> >>> On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < >>> aysam.guerler@gmail.com> wrote: >>> >>>> Hi Rui, >>>> >>>> Are you using the upload tool available in the tool panel under >>>> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >>>> clicking on 'Load Data'? Could you also please let me know if this error >>>> occurs always or just sometimes? >>>> >>>> Thanks Sam >>>> >>>> >>>> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <ruiwang.sz@gmail.com >>>> > wrote: >>>> >>>>> Hi Guys, >>>>> >>>>> Our galaxy instance has been in use for a couple years but since >>>>> Feb 2014 it started to show us some weird behavior. Recently the upload >>>>> function suddenly stopped working properly. We are getting messages like >>>>> the following. I'm not sure if this only happens to us. If someone has seen >>>>> this before, please give me some hints. >>>>> >>>>> P.S., I searched online and many says that this is because the >>>>> browser does not wait till all the data from the server is received and >>>>> closes the socket. However it happens both in firefox and chrome. I'm >>>>> wondering if it is because galaxy has any change recently but when I do 'hg >>>>> update stable' it reported that it is up to date. >>>>> >>>>> Thanks! >>>>> Rui >>>>> >>>>> Error messages: >>>>> >>>>> Exception happened during processing of request from >>>>> ('127.0.0.1'---------------------------------------- >>>>> >>>>> Exception happened during processing of request from (, >>>>> 52259'127.0.0.1', 52260) >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> ) >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> ---------------------------------------- >>>>> >>>>> Exception happened during processing of request from >>>>> (---------------------------------------- >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> Exception happened during processing of request from'127.0.0.1' >>>>> , ('127.0.0.1'52264, 52262---------------------------------------- >>>>> >>>>> ) >>>>> >>>>> Exception happened during processing of request from >>>>> ('127.0.0.1'---------------------------------------- >>>>> >>>>> , ) >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> Exception happened during processing of request from >>>>> 52261('127.0.0.1', ---------------------------------------- >>>>> >>>>> )Exception happened during processing of request from >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> 52263('127.0.0.1') >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> , 52265) >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> Traceback (most recent call last): >>>>> >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>> line 1068, in process_request_in_thread >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> self.finish_request(request, client_address) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>> finish_request >>>>> >>>>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>>>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>>>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> self.finish() >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> self.finish() >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> self.finish() >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> self.RequestHandlerClass(request, client_address, self) >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>> __init__ >>>>> >>>>> self.finish() >>>>> >>>>> self.finish() >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> self.wfile.flush() >>>>> >>>>> self.wfile.flush() >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> self.wfile.flush() >>>>> >>>>> self.finish() >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> self.wfile.flush() >>>>> >>>>> self.finish() >>>>> >>>>> self.wfile.flush() >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> self.wfile.flush() >>>>> >>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> self.wfile.flush() >>>>> >>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> ---------------------------------------- >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> ---------------------------------------- >>>>> >>>>> >>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>> >>>>> ---------------------------------------- >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> ---------------------------------------- >>>>> >>>>> ---------------------------------------- >>>>> >>>>> error: [Errno 32] Broken pipe >>>>> >>>>> ---------------------------------------- >>>>> >>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> http://lists.bx.psu.edu/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >
Hi Rui, I'm not sure what version of the MACS wrapper for Galaxy you were using prior to upgrading, but the version that previously came with the Galaxy distribution, and that is now in the Tool Shed under the devteam account, is only compatible with MACS 1.3.7.1. There is a 1.4 version available in the Tool Shed, but I don't believe anyone on our team has used it. --nate On Tue, Mar 4, 2014 at 8:01 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file=" toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner>
<installed_changeset_revision>ae2ec275332a</installed_changeset_revision> <id> toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1</id> <version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml, we could see that in this dir /home/bioinfoadmin/app/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed=" http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu>wrote:
> Rui, > > could you please try 'hg status' and tell us what it outputs? Thanks > > Martin > > > On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: > >> Hi Martin, >> >> Thanks. I'll read the manual. >> >> Best, >> Rui >> >> >> On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote: >> >>> Hello Rui, >>> >>> the process of migrating tools from Galaxy itself to the ToolShed >>> (Galaxy's appstore) is ongoing and is well described here: >>> https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution >>> >>> Please check the page and let us know if it helps you with your >>> instance. >>> >>> Afterwards we can continue to troubleshoot the upload problems. >>> >>> goodluck >>> >>> Martin >>> >>> >>> On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <ruiwang.sz@gmail.com >>> > wrote: >>> >>>> Hi Sam, >>>> >>>> I used Get Data and Upload file from your computer...and this >>>> just started this Feb, actually a couple days ago it was fine. It happened >>>> always, no matter we load from localhost or remote host, and other means >>>> like paste the path etc didn't work either. >>>> >>>> Actually, I found that there are many released change on the >>>> galaxy release and then I ran a 'hg pull -u'. However I had some error >>>> message saying many of the tools installed are eliminated in the new >>>> distribution and I could install them back from toolshed. I'm quite >>>> confused. >>>> >>>> Here is the command I ran: >>>> >>>> 1. hg pull -u >>>> 2. ./run.sh --daemon (many error msg, follow the >>>> suggestion,then ) >>>> 3. sh manage_db.sh upgrade (update db to 118 version, start >>>> again) >>>> 4. ./run.sh --daemon (many error msg, I'll paste it below, but >>>> next I did) >>>> 5. sh ./scripts/migrate_tools/0009_tools.sh >>>> >>>> now after 5, I run it again, it started, but when I log in, seems >>>> this page is hanging for few hours: >>>> >>>> [image: Inline image 1] >>>> >>>> so the error message in step 4 above was: >>>> >>>> The list of files at the end of this message refers to tools that >>>> are configured to load into the tool panel for >>>> this Galaxy instance, but have been removed from the Galaxy >>>> distribution. These tools and their dependencies can be >>>> automatically installed from the Galaxy tool shed at >>>> http://toolshed.g2.bx.psu.edu. >>>> >>>> To skip this process, attempt to start your Galaxy server again >>>> (e.g., sh run.sh or whatever you use). If you do this, >>>> be aware that these tools will no longer be available in your >>>> Galaxy tool panel, and entries for each of them should >>>> be removed from your file named ./tool_conf.xml >>>> >>>> ...migrate 7->8 >>>> ...migrate 8->9 >>>> >>>> from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu >>>> and will be installed into your local Galaxy instance at the >>>> location discussed above by running the following command. >>>> >>>> >>>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>>> sh ./scripts/migrate_tools/0009_tools.sh >>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>> >>>> The tool dependencies listed above will be installed along with >>>> the repositories if you add the 'install_dependencies' >>>> option to the above command like this: >>>> >>>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>>> sh ./scripts/migrate_tools/0009_tools.sh install_dependencies >>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>> >>>> Tool dependencies can be installed after the repositories have >>>> been installed as well. >>>> >>>> After the installation process finishes, you can start your >>>> Galaxy server. As part of this installation process, >>>> entries for each of the following tool config files will be added >>>> to the file named ./migrated_tool_conf.xml, so these >>>> tools will continue to be loaded into your tool panel. Because >>>> of this, existing entries for these tools have been >>>> removed from your file named ./tool_conf.xml. >>>> >>>> fastq_to_fasta.xml >>>> execute_dwt_var_perFeature.xml >>>> GMAJ.xml >>>> rgWebLogo3.xml >>>> rgClustalw.xml >>>> gi2taxonomy.xml >>>> t2t_report.xml >>>> t2ps_wrapper.xml >>>> find_diag_hits.xml >>>> lca.xml >>>> poisson2test.xml >>>> rgFastQC.xml >>>> fastq_groomer.xml >>>> fastq_paired_end_splitter.xml >>>> fastq_paired_end_joiner.xml >>>> fastq_stats.xml >>>> fastq_combiner.xml >>>> fastq_filter.xml >>>> fastq_trimmer.xml >>>> fastq_trimmer_by_quality.xml >>>> fastq_masker_by_quality.xml >>>> fastq_paired_end_interlacer.xml >>>> fastq_paired_end_deinterlacer.xml >>>> fastq_manipulation.xml >>>> fastq_to_tabular.xml >>>> tabular_to_fastq.xml >>>> bowtie2_wrapper.xml >>>> tophat_wrapper.xml >>>> tophat2_wrapper.xml >>>> express_wrapper.xml >>>> filter_transcripts_via_tracking.xml >>>> macs_wrapper.xml >>>> sicer_wrapper.xml >>>> ccat_wrapper.xml >>>> freebayes.xml >>>> >>>> I ran the command >>>> >>>> sh ./scripts/migrate_tools/0009_tools.sh >>>> >>>> and after that, the start up still shows some errors like: >>>> >>>> galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool >>>> from path: data_source/CR.xml >>>> Traceback (most recent call last): >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>> 502, in load_tool_tag_set >>>> tool = self.load_tool( os.path.join( tool_path, path ), >>>> guid=guid, repository_id=repository_id ) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>> 615, in load_tool >>>> tree = load_tool( config_file ) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>>> in load_tool >>>> tree = parse_xml(path) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>>> in parse_xml >>>> tree = ElementTree.parse(fname) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>> line 859, in parse >>>> tree.parse(source, parser) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>> line 576, in parse >>>> source = open(source, "rb") >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/CR.xml' >>>> galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool >>>> from path: data_source/genomespace_file_browser_prod.xml >>>> Traceback (most recent call last): >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>> 502, in load_tool_tag_set >>>> tool = self.load_tool( os.path.join( tool_path, path ), >>>> guid=guid, repository_id=repository_id ) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>> 615, in load_tool >>>> tree = load_tool( config_file ) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>>> in load_tool >>>> tree = parse_xml(path) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>>> in parse_xml >>>> tree = ElementTree.parse(fname) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>> line 859, in parse >>>> tree.parse(source, parser) >>>> File >>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>> line 576, in parse >>>> source = open(source, "rb") >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/genomespace_file_browser_prod.xml' >>>> galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool >>>> peakcalling_macs: a when tag has been defined for 'genome_size_cond >>>> (genome_size) --> 90300000', but does not appear to be selectable. >>>> >>>> now if I do a 'grep IOError paster.log', I got the following: >>>> >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/CR.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/genomespace_file_browser_prod.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/bx_browser.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/flymine.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/flymine_test.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/modmine.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/mousemine.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/ratmine.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/yeastmine.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/metabolicmine.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/encode_db.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/epigraph_import.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_source/epigraph_import_test.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_destination/epigraph.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/data_destination/epigraph_test.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/encode/gencode_partition.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/encode/random_intervals.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/new_operations/column_join.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/extract/phastOdds/phastOdds_tool.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/t_test_two_samples.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/plotting/xy_plot.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/getIndels_3way.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/delete_overlapping_indels.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/compute_motifs_frequency.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/categorize_elements_satisfying_criteria.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/draw_stacked_barplots.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/regVariation/microsatellite_birthdeath.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/hyphy/hyphy_branch_lengths_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/hyphy/hyphy_nj_tree_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/hyphy/hyphy_dnds_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/evolution/mutate_snp_codon.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fasta_formatter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fasta_nucleotide_changer.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_collapser.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastq_quality_converter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_quality_statistics.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastq_quality_boxplot.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastq_quality_filter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_artifacts_filter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_barcode_splitter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_clipper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_collapser.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_renamer.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_reverse_complement.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/fastx_toolkit/fastx_trimmer.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/indels/sam_indel_filter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/indels/indel_sam2interval.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/indels/indel_table.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/indels/indel_analysis.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/ngs_rna/tophat_color_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/ngs_rna/cufflinks_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/ngs_rna/cuffcompare_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/ngs_rna/cuffmerge_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/ngs_rna/cuffdiff_wrapper.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/sam_bitwise_flag_filter.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/sam2interval.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/sam_to_bam.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/bam_to_sam.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/sam_merge.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/samtools_mpileup.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/sam_pileup.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/pileup_parser.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/pileup_interval.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/samtools_flagstat.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/samtools_rmdup.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/samtools/samtools_slice_bam.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/genetrack/genetrack_indexer.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/genetrack/genetrack_peak_prediction.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgClean.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgPedSub.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgLDIndep.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgfakePhe.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgfakePed.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgQC.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgEigPCA.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgHaploView.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgManQQ.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgGRR.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgCaCo.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgTDT.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgGLM.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/rgenetics/rgManQQ.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/phenotype_association/ctd.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/phenotype_association/funDo.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/phenotype_association/hilbertvis.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/phenotype_association/dividePgSnpAlleles.xml' >>>> IOError: [Errno 2] No such file or directory: >>>> './tools/vcf_tools/intersect.xml' >>>> >>>> I'm not sure if I successfully updated galaxy source...since >>>> right now the screen is always hanging. I think I miss some config files or >>>> so. >>>> >>>> Could you please advise? >>>> >>>> Thanks, >>>> Rui >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < >>>> aysam.guerler@gmail.com> wrote: >>>> >>>>> Hi Rui, >>>>> >>>>> Are you using the upload tool available in the tool panel under >>>>> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >>>>> clicking on 'Load Data'? Could you also please let me know if this error >>>>> occurs always or just sometimes? >>>>> >>>>> Thanks Sam >>>>> >>>>> >>>>> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz < >>>>> ruiwang.sz@gmail.com> wrote: >>>>> >>>>>> Hi Guys, >>>>>> >>>>>> Our galaxy instance has been in use for a couple years but >>>>>> since Feb 2014 it started to show us some weird behavior. Recently the >>>>>> upload function suddenly stopped working properly. We are getting messages >>>>>> like the following. I'm not sure if this only happens to us. If someone has >>>>>> seen this before, please give me some hints. >>>>>> >>>>>> P.S., I searched online and many says that this is because the >>>>>> browser does not wait till all the data from the server is received and >>>>>> closes the socket. However it happens both in firefox and chrome. I'm >>>>>> wondering if it is because galaxy has any change recently but when I do 'hg >>>>>> update stable' it reported that it is up to date. >>>>>> >>>>>> Thanks! >>>>>> Rui >>>>>> >>>>>> Error messages: >>>>>> >>>>>> Exception happened during processing of request from >>>>>> ('127.0.0.1'---------------------------------------- >>>>>> >>>>>> Exception happened during processing of request from (, >>>>>> 52259'127.0.0.1', 52260) >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> ) >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> Exception happened during processing of request from >>>>>> (---------------------------------------- >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> Exception happened during processing of request from'127.0.0.1' >>>>>> , ('127.0.0.1'52264, 52262---------------------------------------- >>>>>> >>>>>> ) >>>>>> >>>>>> Exception happened during processing of request from >>>>>> ('127.0.0.1'---------------------------------------- >>>>>> >>>>>> , ) >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> Exception happened during processing of request from >>>>>> 52261('127.0.0.1', ---------------------------------------- >>>>>> >>>>>> )Exception happened during processing of request from >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> 52263('127.0.0.1') >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> , 52265) >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> Traceback (most recent call last): >>>>>> >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>> line 1068, in process_request_in_thread >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> self.finish_request(request, client_address) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>> finish_request >>>>>> >>>>>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>>>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>>>>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>>>>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> self.finish() >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> self.finish() >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> self.finish() >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>> __init__ >>>>>> >>>>>> self.finish() >>>>>> >>>>>> self.finish() >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> self.finish() >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> self.finish() >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> self.wfile.flush() >>>>>> >>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> >>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> error: [Errno 32] Broken pipe >>>>>> >>>>>> ---------------------------------------- >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ___________________________________________________________ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> http://lists.bx.psu.edu/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>>>> >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> http://lists.bx.psu.edu/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Nate, Thanks for the note!! The wrapper we were using prior to upgrading was 1.0.0, and now the wrapper in toolshed is 1.0.1. I could not switch between them -- an error occurred. However, the MACS binary package I installed had the name of executable file 'macs14', I thought that it is 1.4? Here people use it all the time. So in short, now I still have the 1.4 installed, but shed_tool has the 1.3.7.1. How could I let Galaxy still use 1.4? Do I need to remove the shed_tool version by uninstalling that repo? I guess this might be a general question: how do I manage multiple version of tools from different sources(shed_tool and own installation)? Best Regards, Rui On Fri, Mar 7, 2014 at 6:10 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Rui,
I'm not sure what version of the MACS wrapper for Galaxy you were using prior to upgrading, but the version that previously came with the Galaxy distribution, and that is now in the Tool Shed under the devteam account, is only compatible with MACS 1.3.7.1. There is a 1.4 version available in the Tool Shed, but I don't believe anyone on our team has used it.
--nate
On Tue, Mar 4, 2014 at 8:01 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file=" toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner>
<installed_changeset_revision>ae2ec275332a</installed_changeset_revision> <id> toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1</id> <version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml, we could see that in this dir /home/bioinfoadmin/app/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed=" http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu>wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
> Hi Martin, > > Here you go. there are 493 files missing, seems. > > Thanks, > Rui > > > On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu>wrote: > >> Rui, >> >> could you please try 'hg status' and tell us what it outputs? Thanks >> >> Martin >> >> >> On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: >> >>> Hi Martin, >>> >>> Thanks. I'll read the manual. >>> >>> Best, >>> Rui >>> >>> >>> On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote: >>> >>>> Hello Rui, >>>> >>>> the process of migrating tools from Galaxy itself to the ToolShed >>>> (Galaxy's appstore) is ongoing and is well described here: >>>> https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution >>>> >>>> Please check the page and let us know if it helps you with your >>>> instance. >>>> >>>> Afterwards we can continue to troubleshoot the upload problems. >>>> >>>> goodluck >>>> >>>> Martin >>>> >>>> >>>> On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz < >>>> ruiwang.sz@gmail.com> wrote: >>>> >>>>> Hi Sam, >>>>> >>>>> I used Get Data and Upload file from your computer...and this >>>>> just started this Feb, actually a couple days ago it was fine. It happened >>>>> always, no matter we load from localhost or remote host, and other means >>>>> like paste the path etc didn't work either. >>>>> >>>>> Actually, I found that there are many released change on the >>>>> galaxy release and then I ran a 'hg pull -u'. However I had some error >>>>> message saying many of the tools installed are eliminated in the new >>>>> distribution and I could install them back from toolshed. I'm quite >>>>> confused. >>>>> >>>>> Here is the command I ran: >>>>> >>>>> 1. hg pull -u >>>>> 2. ./run.sh --daemon (many error msg, follow the >>>>> suggestion,then ) >>>>> 3. sh manage_db.sh upgrade (update db to 118 version, start >>>>> again) >>>>> 4. ./run.sh --daemon (many error msg, I'll paste it below, >>>>> but next I did) >>>>> 5. sh ./scripts/migrate_tools/0009_tools.sh >>>>> >>>>> now after 5, I run it again, it started, but when I log in, >>>>> seems this page is hanging for few hours: >>>>> >>>>> [image: Inline image 1] >>>>> >>>>> so the error message in step 4 above was: >>>>> >>>>> The list of files at the end of this message refers to tools >>>>> that are configured to load into the tool panel for >>>>> this Galaxy instance, but have been removed from the Galaxy >>>>> distribution. These tools and their dependencies can be >>>>> automatically installed from the Galaxy tool shed at >>>>> http://toolshed.g2.bx.psu.edu. >>>>> >>>>> To skip this process, attempt to start your Galaxy server again >>>>> (e.g., sh run.sh or whatever you use). If you do this, >>>>> be aware that these tools will no longer be available in your >>>>> Galaxy tool panel, and entries for each of them should >>>>> be removed from your file named ./tool_conf.xml >>>>> >>>>> ...migrate 7->8 >>>>> ...migrate 8->9 >>>>> >>>>> from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu >>>>> and will be installed into your local Galaxy instance at the >>>>> location discussed above by running the following command. >>>>> >>>>> >>>>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>>>> sh ./scripts/migrate_tools/0009_tools.sh >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> >>>>> The tool dependencies listed above will be installed along with >>>>> the repositories if you add the 'install_dependencies' >>>>> option to the above command like this: >>>>> >>>>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>>>> sh ./scripts/migrate_tools/0009_tools.sh install_dependencies >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> >>>>> Tool dependencies can be installed after the repositories have >>>>> been installed as well. >>>>> >>>>> After the installation process finishes, you can start your >>>>> Galaxy server. As part of this installation process, >>>>> entries for each of the following tool config files will be >>>>> added to the file named ./migrated_tool_conf.xml, so these >>>>> tools will continue to be loaded into your tool panel. Because >>>>> of this, existing entries for these tools have been >>>>> removed from your file named ./tool_conf.xml. >>>>> >>>>> fastq_to_fasta.xml >>>>> execute_dwt_var_perFeature.xml >>>>> GMAJ.xml >>>>> rgWebLogo3.xml >>>>> rgClustalw.xml >>>>> gi2taxonomy.xml >>>>> t2t_report.xml >>>>> t2ps_wrapper.xml >>>>> find_diag_hits.xml >>>>> lca.xml >>>>> poisson2test.xml >>>>> rgFastQC.xml >>>>> fastq_groomer.xml >>>>> fastq_paired_end_splitter.xml >>>>> fastq_paired_end_joiner.xml >>>>> fastq_stats.xml >>>>> fastq_combiner.xml >>>>> fastq_filter.xml >>>>> fastq_trimmer.xml >>>>> fastq_trimmer_by_quality.xml >>>>> fastq_masker_by_quality.xml >>>>> fastq_paired_end_interlacer.xml >>>>> fastq_paired_end_deinterlacer.xml >>>>> fastq_manipulation.xml >>>>> fastq_to_tabular.xml >>>>> tabular_to_fastq.xml >>>>> bowtie2_wrapper.xml >>>>> tophat_wrapper.xml >>>>> tophat2_wrapper.xml >>>>> express_wrapper.xml >>>>> filter_transcripts_via_tracking.xml >>>>> macs_wrapper.xml >>>>> sicer_wrapper.xml >>>>> ccat_wrapper.xml >>>>> freebayes.xml >>>>> >>>>> I ran the command >>>>> >>>>> sh ./scripts/migrate_tools/0009_tools.sh >>>>> >>>>> and after that, the start up still shows some errors like: >>>>> >>>>> galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool >>>>> from path: data_source/CR.xml >>>>> Traceback (most recent call last): >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>> 502, in load_tool_tag_set >>>>> tool = self.load_tool( os.path.join( tool_path, path ), >>>>> guid=guid, repository_id=repository_id ) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>> 615, in load_tool >>>>> tree = load_tool( config_file ) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>>>> in load_tool >>>>> tree = parse_xml(path) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>>>> in parse_xml >>>>> tree = ElementTree.parse(fname) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>> line 859, in parse >>>>> tree.parse(source, parser) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>> line 576, in parse >>>>> source = open(source, "rb") >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/CR.xml' >>>>> galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool >>>>> from path: data_source/genomespace_file_browser_prod.xml >>>>> Traceback (most recent call last): >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>> 502, in load_tool_tag_set >>>>> tool = self.load_tool( os.path.join( tool_path, path ), >>>>> guid=guid, repository_id=repository_id ) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>> 615, in load_tool >>>>> tree = load_tool( config_file ) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>>>> in load_tool >>>>> tree = parse_xml(path) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>>>> in parse_xml >>>>> tree = ElementTree.parse(fname) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>> line 859, in parse >>>>> tree.parse(source, parser) >>>>> File >>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>> line 576, in parse >>>>> source = open(source, "rb") >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/genomespace_file_browser_prod.xml' >>>>> galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool >>>>> peakcalling_macs: a when tag has been defined for 'genome_size_cond >>>>> (genome_size) --> 90300000', but does not appear to be selectable. >>>>> >>>>> now if I do a 'grep IOError paster.log', I got the following: >>>>> >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/CR.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/genomespace_file_browser_prod.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/bx_browser.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/flymine.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/flymine_test.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/modmine.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/mousemine.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/ratmine.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/yeastmine.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/metabolicmine.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/encode_db.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/epigraph_import.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_source/epigraph_import_test.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_destination/epigraph.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/data_destination/epigraph_test.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/encode/gencode_partition.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/encode/random_intervals.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/new_operations/column_join.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/extract/phastOdds/phastOdds_tool.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/t_test_two_samples.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/plotting/xy_plot.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/getIndels_3way.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/delete_overlapping_indels.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/compute_motifs_frequency.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/categorize_elements_satisfying_criteria.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/draw_stacked_barplots.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/regVariation/microsatellite_birthdeath.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/hyphy/hyphy_branch_lengths_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/hyphy/hyphy_nj_tree_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/hyphy/hyphy_dnds_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/evolution/mutate_snp_codon.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fasta_formatter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fasta_nucleotide_changer.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_collapser.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastq_quality_converter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_quality_statistics.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastq_quality_boxplot.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastq_quality_filter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_artifacts_filter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_barcode_splitter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_clipper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_collapser.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_renamer.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_reverse_complement.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/fastx_toolkit/fastx_trimmer.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/indels/sam_indel_filter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/indels/indel_sam2interval.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/indels/indel_table.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/indels/indel_analysis.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/ngs_rna/tophat_color_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/ngs_rna/cufflinks_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/ngs_rna/cuffcompare_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/ngs_rna/cuffmerge_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/ngs_rna/cuffdiff_wrapper.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/sam_bitwise_flag_filter.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/sam2interval.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/sam_to_bam.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/bam_to_sam.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/sam_merge.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/samtools_mpileup.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/sam_pileup.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/pileup_parser.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/pileup_interval.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/samtools_flagstat.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/samtools_rmdup.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/samtools/samtools_slice_bam.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/genetrack/genetrack_indexer.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/genetrack/genetrack_peak_prediction.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgClean.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgPedSub.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgLDIndep.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgfakePhe.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgfakePed.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgQC.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgEigPCA.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgHaploView.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgManQQ.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgGRR.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgCaCo.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgTDT.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgGLM.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/rgenetics/rgManQQ.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/phenotype_association/ctd.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/phenotype_association/funDo.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/phenotype_association/hilbertvis.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/phenotype_association/dividePgSnpAlleles.xml' >>>>> IOError: [Errno 2] No such file or directory: >>>>> './tools/vcf_tools/intersect.xml' >>>>> >>>>> I'm not sure if I successfully updated galaxy source...since >>>>> right now the screen is always hanging. I think I miss some config files or >>>>> so. >>>>> >>>>> Could you please advise? >>>>> >>>>> Thanks, >>>>> Rui >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < >>>>> aysam.guerler@gmail.com> wrote: >>>>> >>>>>> Hi Rui, >>>>>> >>>>>> Are you using the upload tool available in the tool panel under >>>>>> 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by >>>>>> clicking on 'Load Data'? Could you also please let me know if this error >>>>>> occurs always or just sometimes? >>>>>> >>>>>> Thanks Sam >>>>>> >>>>>> >>>>>> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz < >>>>>> ruiwang.sz@gmail.com> wrote: >>>>>> >>>>>>> Hi Guys, >>>>>>> >>>>>>> Our galaxy instance has been in use for a couple years but >>>>>>> since Feb 2014 it started to show us some weird behavior. Recently the >>>>>>> upload function suddenly stopped working properly. We are getting messages >>>>>>> like the following. I'm not sure if this only happens to us. If someone has >>>>>>> seen this before, please give me some hints. >>>>>>> >>>>>>> P.S., I searched online and many says that this is because the >>>>>>> browser does not wait till all the data from the server is received and >>>>>>> closes the socket. However it happens both in firefox and chrome. I'm >>>>>>> wondering if it is because galaxy has any change recently but when I do 'hg >>>>>>> update stable' it reported that it is up to date. >>>>>>> >>>>>>> Thanks! >>>>>>> Rui >>>>>>> >>>>>>> Error messages: >>>>>>> >>>>>>> Exception happened during processing of request from >>>>>>> ('127.0.0.1'---------------------------------------- >>>>>>> >>>>>>> Exception happened during processing of request from (, >>>>>>> 52259'127.0.0.1', 52260) >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> ) >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> Exception happened during processing of request from >>>>>>> (---------------------------------------- >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> Exception happened during processing of request >>>>>>> from'127.0.0.1' , ('127.0.0.1'52264, >>>>>>> 52262---------------------------------------- >>>>>>> >>>>>>> ) >>>>>>> >>>>>>> Exception happened during processing of request from >>>>>>> ('127.0.0.1'---------------------------------------- >>>>>>> >>>>>>> , ) >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> Exception happened during processing of request from >>>>>>> 52261('127.0.0.1', ---------------------------------------- >>>>>>> >>>>>>> )Exception happened during processing of request from >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> 52263('127.0.0.1') >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> , 52265) >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> >>>>>>> File >>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>> line 1068, in process_request_in_thread >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> self.finish_request(request, client_address) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>> finish_request >>>>>>> >>>>>>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>>>>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>>>>>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux >>>>>>> x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>> __init__ >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> self.finish() >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>> finish >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> self.wfile.flush() >>>>>>> >>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> >>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> error: [Errno 32] Broken pipe >>>>>>> >>>>>>> ---------------------------------------- >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ___________________________________________________________ >>>>>>> Please keep all replies on the list by using "reply all" >>>>>>> in your mail client. To manage your subscriptions to this >>>>>>> and other Galaxy lists, please use the interface at: >>>>>>> http://lists.bx.psu.edu/ >>>>>>> >>>>>>> To search Galaxy mailing lists use the unified search at: >>>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>>> >>>>>> >>>>>> >>>>> >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> http://lists.bx.psu.edu/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>>> >>> >> >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again. imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy? If there is some subtler problem with an incorrect version of MACS being used by a tool - that is definitely fixable, Galaxy can resolve requirements in a very configurable manner so let me know - but that is not sounding like the problem you are having. -John On Fri, Mar 7, 2014 at 10:43 AM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Nate,
Thanks for the note!!
The wrapper we were using prior to upgrading was 1.0.0, and now the wrapper in toolshed is 1.0.1. I could not switch between them -- an error occurred.
However, the MACS binary package I installed had the name of executable file 'macs14', I thought that it is 1.4? Here people use it all the time.
So in short, now I still have the 1.4 installed, but shed_tool has the 1.3.7.1. How could I let Galaxy still use 1.4? Do I need to remove the shed_tool version by uninstalling that repo? I guess this might be a general question: how do I manage multiple version of tools from different sources(shed_tool and own installation)?
Best Regards, Rui
On Fri, Mar 7, 2014 at 6:10 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Rui,
I'm not sure what version of the MACS wrapper for Galaxy you were using prior to upgrading, but the version that previously came with the Galaxy distribution, and that is now in the Tool Shed under the devteam account, is only compatible with MACS 1.3.7.1. There is a 1.4 version available in the Tool Shed, but I don't believe anyone on our team has used it.
--nate
On Tue, Mar 4, 2014 at 8:01 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file=" toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner>
<installed_changeset_revision>ae2ec275332a</installed_changeset_revision> <id> toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1</id> <version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml, we could see that in this dir /home/bioinfoadmin/app/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed=" http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu>wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <ruiwang.sz@gmail.com>wrote:
> oh, I took that back, I think these are the tools that I installed > but does not come with Galaxy. probably that's the ? means -- it is not > part of the distribution? > > thanks, > Rui > > > On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <ruiwang.sz@gmail.com>wrote: > >> Hi Martin, >> >> Here you go. there are 493 files missing, seems. >> >> Thanks, >> Rui >> >> >> On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu>wrote: >> >>> Rui, >>> >>> could you please try 'hg status' and tell us what it outputs? >>> Thanks >>> >>> Martin >>> >>> >>> On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <ruiwang.sz@gmail.com >>> > wrote: >>> >>>> Hi Martin, >>>> >>>> Thanks. I'll read the manual. >>>> >>>> Best, >>>> Rui >>>> >>>> >>>> On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu>wrote: >>>> >>>>> Hello Rui, >>>>> >>>>> the process of migrating tools from Galaxy itself to the >>>>> ToolShed (Galaxy's appstore) is ongoing and is well described here: >>>>> https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution >>>>> >>>>> Please check the page and let us know if it helps you with your >>>>> instance. >>>>> >>>>> Afterwards we can continue to troubleshoot the upload problems. >>>>> >>>>> goodluck >>>>> >>>>> Martin >>>>> >>>>> >>>>> On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz < >>>>> ruiwang.sz@gmail.com> wrote: >>>>> >>>>>> Hi Sam, >>>>>> >>>>>> I used Get Data and Upload file from your computer...and this >>>>>> just started this Feb, actually a couple days ago it was fine. It happened >>>>>> always, no matter we load from localhost or remote host, and other means >>>>>> like paste the path etc didn't work either. >>>>>> >>>>>> Actually, I found that there are many released change on the >>>>>> galaxy release and then I ran a 'hg pull -u'. However I had some error >>>>>> message saying many of the tools installed are eliminated in the new >>>>>> distribution and I could install them back from toolshed. I'm quite >>>>>> confused. >>>>>> >>>>>> Here is the command I ran: >>>>>> >>>>>> 1. hg pull -u >>>>>> 2. ./run.sh --daemon (many error msg, follow the >>>>>> suggestion,then ) >>>>>> 3. sh manage_db.sh upgrade (update db to 118 version, >>>>>> start again) >>>>>> 4. ./run.sh --daemon (many error msg, I'll paste it below, >>>>>> but next I did) >>>>>> 5. sh ./scripts/migrate_tools/0009_tools.sh >>>>>> >>>>>> now after 5, I run it again, it started, but when I log in, >>>>>> seems this page is hanging for few hours: >>>>>> >>>>>> [image: Inline image 1] >>>>>> >>>>>> so the error message in step 4 above was: >>>>>> >>>>>> The list of files at the end of this message refers to tools >>>>>> that are configured to load into the tool panel for >>>>>> this Galaxy instance, but have been removed from the Galaxy >>>>>> distribution. These tools and their dependencies can be >>>>>> automatically installed from the Galaxy tool shed at >>>>>> http://toolshed.g2.bx.psu.edu. >>>>>> >>>>>> To skip this process, attempt to start your Galaxy server again >>>>>> (e.g., sh run.sh or whatever you use). If you do this, >>>>>> be aware that these tools will no longer be available in your >>>>>> Galaxy tool panel, and entries for each of them should >>>>>> be removed from your file named ./tool_conf.xml >>>>>> >>>>>> ...migrate 7->8 >>>>>> ...migrate 8->9 >>>>>> >>>>>> from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu >>>>>> and will be installed into your local Galaxy instance at the >>>>>> location discussed above by running the following command. >>>>>> >>>>>> >>>>>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>>>>> sh ./scripts/migrate_tools/0009_tools.sh >>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>> >>>>>> The tool dependencies listed above will be installed along with >>>>>> the repositories if you add the 'install_dependencies' >>>>>> option to the above command like this: >>>>>> >>>>>> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv >>>>>> sh ./scripts/migrate_tools/0009_tools.sh install_dependencies >>>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>>> >>>>>> Tool dependencies can be installed after the repositories have >>>>>> been installed as well. >>>>>> >>>>>> After the installation process finishes, you can start your >>>>>> Galaxy server. As part of this installation process, >>>>>> entries for each of the following tool config files will be >>>>>> added to the file named ./migrated_tool_conf.xml, so these >>>>>> tools will continue to be loaded into your tool panel. Because >>>>>> of this, existing entries for these tools have been >>>>>> removed from your file named ./tool_conf.xml. >>>>>> >>>>>> fastq_to_fasta.xml >>>>>> execute_dwt_var_perFeature.xml >>>>>> GMAJ.xml >>>>>> rgWebLogo3.xml >>>>>> rgClustalw.xml >>>>>> gi2taxonomy.xml >>>>>> t2t_report.xml >>>>>> t2ps_wrapper.xml >>>>>> find_diag_hits.xml >>>>>> lca.xml >>>>>> poisson2test.xml >>>>>> rgFastQC.xml >>>>>> fastq_groomer.xml >>>>>> fastq_paired_end_splitter.xml >>>>>> fastq_paired_end_joiner.xml >>>>>> fastq_stats.xml >>>>>> fastq_combiner.xml >>>>>> fastq_filter.xml >>>>>> fastq_trimmer.xml >>>>>> fastq_trimmer_by_quality.xml >>>>>> fastq_masker_by_quality.xml >>>>>> fastq_paired_end_interlacer.xml >>>>>> fastq_paired_end_deinterlacer.xml >>>>>> fastq_manipulation.xml >>>>>> fastq_to_tabular.xml >>>>>> tabular_to_fastq.xml >>>>>> bowtie2_wrapper.xml >>>>>> tophat_wrapper.xml >>>>>> tophat2_wrapper.xml >>>>>> express_wrapper.xml >>>>>> filter_transcripts_via_tracking.xml >>>>>> macs_wrapper.xml >>>>>> sicer_wrapper.xml >>>>>> ccat_wrapper.xml >>>>>> freebayes.xml >>>>>> >>>>>> I ran the command >>>>>> >>>>>> sh ./scripts/migrate_tools/0009_tools.sh >>>>>> >>>>>> and after that, the start up still shows some errors like: >>>>>> >>>>>> galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool >>>>>> from path: data_source/CR.xml >>>>>> Traceback (most recent call last): >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>>> 502, in load_tool_tag_set >>>>>> tool = self.load_tool( os.path.join( tool_path, path ), >>>>>> guid=guid, repository_id=repository_id ) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>>> 615, in load_tool >>>>>> tree = load_tool( config_file ) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>>>>> in load_tool >>>>>> tree = parse_xml(path) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>>>>> in parse_xml >>>>>> tree = ElementTree.parse(fname) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>>> line 859, in parse >>>>>> tree.parse(source, parser) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>>> line 576, in parse >>>>>> source = open(source, "rb") >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/CR.xml' >>>>>> galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool >>>>>> from path: data_source/genomespace_file_browser_prod.xml >>>>>> Traceback (most recent call last): >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>>> 502, in load_tool_tag_set >>>>>> tool = self.load_tool( os.path.join( tool_path, path ), >>>>>> guid=guid, repository_id=repository_id ) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line >>>>>> 615, in load_tool >>>>>> tree = load_tool( config_file ) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, >>>>>> in load_tool >>>>>> tree = parse_xml(path) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, >>>>>> in parse_xml >>>>>> tree = ElementTree.parse(fname) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>>> line 859, in parse >>>>>> tree.parse(source, parser) >>>>>> File >>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", >>>>>> line 576, in parse >>>>>> source = open(source, "rb") >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/genomespace_file_browser_prod.xml' >>>>>> galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool >>>>>> peakcalling_macs: a when tag has been defined for 'genome_size_cond >>>>>> (genome_size) --> 90300000', but does not appear to be selectable. >>>>>> >>>>>> now if I do a 'grep IOError paster.log', I got the following: >>>>>> >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/CR.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/genomespace_file_browser_prod.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/bx_browser.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/flymine.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/flymine_test.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/modmine.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/mousemine.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/ratmine.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/yeastmine.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/metabolicmine.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/encode_db.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/epigraph_import.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_source/epigraph_import_test.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_destination/epigraph.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/data_destination/epigraph_test.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/encode/gencode_partition.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/encode/random_intervals.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/new_operations/column_join.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/extract/phastOdds/phastOdds_tool.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/t_test_two_samples.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/plotting/xy_plot.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/getIndels_3way.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/delete_overlapping_indels.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/compute_motifs_frequency.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/categorize_elements_satisfying_criteria.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/draw_stacked_barplots.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/regVariation/microsatellite_birthdeath.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/hyphy/hyphy_branch_lengths_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/hyphy/hyphy_nj_tree_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/hyphy/hyphy_dnds_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/evolution/mutate_snp_codon.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fasta_formatter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fasta_nucleotide_changer.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_collapser.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastq_quality_converter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_quality_statistics.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastq_quality_boxplot.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastq_quality_filter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_artifacts_filter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_barcode_splitter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_clipper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_collapser.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_renamer.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_reverse_complement.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/fastx_toolkit/fastx_trimmer.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/indels/sam_indel_filter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/indels/indel_sam2interval.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/indels/indel_table.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/indels/indel_analysis.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/ngs_rna/tophat_color_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/ngs_rna/cufflinks_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/ngs_rna/cuffcompare_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/ngs_rna/cuffmerge_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/ngs_rna/cuffdiff_wrapper.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/sam_bitwise_flag_filter.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/sam2interval.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/sam_to_bam.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/bam_to_sam.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/sam_merge.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/samtools_mpileup.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/sam_pileup.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/pileup_parser.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/pileup_interval.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/samtools_flagstat.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/samtools_rmdup.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/samtools/samtools_slice_bam.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/genetrack/genetrack_indexer.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/genetrack/genetrack_peak_prediction.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgClean.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgPedSub.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgLDIndep.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgfakePhe.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgfakePed.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgQC.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgEigPCA.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgHaploView.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgManQQ.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgGRR.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgCaCo.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgTDT.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgGLM.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/rgenetics/rgManQQ.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/phenotype_association/ctd.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/phenotype_association/funDo.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/phenotype_association/hilbertvis.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/phenotype_association/dividePgSnpAlleles.xml' >>>>>> IOError: [Errno 2] No such file or directory: >>>>>> './tools/vcf_tools/intersect.xml' >>>>>> >>>>>> I'm not sure if I successfully updated galaxy source...since >>>>>> right now the screen is always hanging. I think I miss some config files or >>>>>> so. >>>>>> >>>>>> Could you please advise? >>>>>> >>>>>> Thanks, >>>>>> Rui >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Feb 27, 2014 at 7:21 PM, sam guerler < >>>>>> aysam.guerler@gmail.com> wrote: >>>>>> >>>>>>> Hi Rui, >>>>>>> >>>>>>> Are you using the upload tool available in the tool panel >>>>>>> under 'Get Data' > 'Upload file from your computer'? Or the new upload >>>>>>> dialog by clicking on 'Load Data'? Could you also please let me know if >>>>>>> this error occurs always or just sometimes? >>>>>>> >>>>>>> Thanks Sam >>>>>>> >>>>>>> >>>>>>> On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz < >>>>>>> ruiwang.sz@gmail.com> wrote: >>>>>>> >>>>>>>> Hi Guys, >>>>>>>> >>>>>>>> Our galaxy instance has been in use for a couple years but >>>>>>>> since Feb 2014 it started to show us some weird behavior. Recently the >>>>>>>> upload function suddenly stopped working properly. We are getting messages >>>>>>>> like the following. I'm not sure if this only happens to us. If someone has >>>>>>>> seen this before, please give me some hints. >>>>>>>> >>>>>>>> P.S., I searched online and many says that this is because >>>>>>>> the browser does not wait till all the data from the server is received and >>>>>>>> closes the socket. However it happens both in firefox and chrome. I'm >>>>>>>> wondering if it is because galaxy has any change recently but when I do 'hg >>>>>>>> update stable' it reported that it is up to date. >>>>>>>> >>>>>>>> Thanks! >>>>>>>> Rui >>>>>>>> >>>>>>>> Error messages: >>>>>>>> >>>>>>>> Exception happened during processing of request from >>>>>>>> ('127.0.0.1'---------------------------------------- >>>>>>>> >>>>>>>> Exception happened during processing of request from (, >>>>>>>> 52259'127.0.0.1', 52260) >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> ) >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> Exception happened during processing of request from >>>>>>>> (---------------------------------------- >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> Exception happened during processing of request >>>>>>>> from'127.0.0.1' , ('127.0.0.1'52264, >>>>>>>> 52262---------------------------------------- >>>>>>>> >>>>>>>> ) >>>>>>>> >>>>>>>> Exception happened during processing of request from >>>>>>>> ('127.0.0.1'---------------------------------------- >>>>>>>> >>>>>>>> , ) >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> Exception happened during processing of request from >>>>>>>> 52261('127.0.0.1', ---------------------------------------- >>>>>>>> >>>>>>>> )Exception happened during processing of request from >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> 52263('127.0.0.1') >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> , 52265) >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> >>>>>>>> File >>>>>>>> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", >>>>>>>> line 1068, in process_request_in_thread >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> self.finish_request(request, client_address) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 323, in >>>>>>>> finish_request >>>>>>>> >>>>>>>> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET >>>>>>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - " >>>>>>>> http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; >>>>>>>> Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> self.RequestHandlerClass(request, client_address, self) >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 640, in >>>>>>>> __init__ >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> self.finish() >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/SocketServer.py", line 693, in >>>>>>>> finish >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> self.wfile.flush() >>>>>>>> >>>>>>>> File "/usr/lib/python2.7/socket.py", line 303, in flush >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> self._sock.sendall(view[write_offset:write_offset+buffer_size]) >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> error: [Errno 32] Broken pipe >>>>>>>> >>>>>>>> ---------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ___________________________________________________________ >>>>>>>> Please keep all replies on the list by using "reply all" >>>>>>>> in your mail client. To manage your subscriptions to this >>>>>>>> and other Galaxy lists, please use the interface at: >>>>>>>> http://lists.bx.psu.edu/ >>>>>>>> >>>>>>>> To search Galaxy mailing lists use the unified search at: >>>>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> ___________________________________________________________ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> http://lists.bx.psu.edu/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>>>> >>>> >>> >> >
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Hi John, Thanks for the note. Please see inline. On Fri, Mar 7, 2014 at 7:18 PM, John Chilton <jmchilton@gmail.com> wrote:
Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again. imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy?
Yes that's what I thought, but I was worrying that if I remove devteam version of macs from the migrated_tool.conf, I might break something potentially useful for galaxy. Mainly, I try not to manually change things since that would not be maintainable over time. That's why I was asking how to handle this properly. It's great to have your confirmation that it works this way. :-) Thanks, Rui
Awesome. How is the upload behaving? Are you still having issues with it? M. On Sat, Mar 8, 2014 at 12:20 PM, ruiwang.sz <ruiwang.sz@gmail.com> wrote:
Hi John,
Thanks for the note. Please see inline.
On Fri, Mar 7, 2014 at 7:18 PM, John Chilton <jmchilton@gmail.com> wrote:
Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again. imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy?
Yes that's what I thought, but I was worrying that if I remove devteam version of macs from the migrated_tool.conf, I might break something potentially useful for galaxy. Mainly, I try not to manually change things since that would not be maintainable over time. That's why I was asking how to handle this properly. It's great to have your confirmation that it works this way. :-)
Thanks, Rui
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Hi, I also have problems with macs and macs2 after update. I got this error which seems a python version issue. But I can not find this file. File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson Any suggestions? Thanks a lot. Changyu Traceback (most recent call last): File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py", line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py", line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
Hi, I also have problems with macs and macs2 with updated galaxy. I got this error which seems a python version issue. But I can not find this file. File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson Any suggestions? Thanks a lot. Changyu Traceback (most recent call last): File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py", line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py", line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson On 3/4/14 8:01 PM, ruiwang.sz wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1>"> <tool_shed>toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>ae2ec275332a</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1></id> <version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>, we could see that in this dir /home/bioinfoadmin/app/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs>, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin C(ech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin C(ech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin C(ech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin C(ech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
Inline image 1
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com <mailto:aysam.guerler@gmail.com>> wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Hi, can you point me to the MACS2 wrapper you are using? If you find the correct wrapper file you can simply replace simplejson with json and it should work. Thanks, Bjoern Am 13.03.2014 13:22, schrieb changyu:
Hi, I also have problems with macs and macs2 with updated galaxy. I got this error which seems a python version issue. But I can not find this file.
File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
Any suggestions?
Thanks a lot.
Changyu
Traceback (most recent call last): File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py", line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py", line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
On 3/4/14 8:01 PM, ruiwang.sz wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>" guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1>"> <tool_shed>toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>ae2ec275332a</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1></id> <version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>, we could see that in this dir /home/bioinfoadmin/app/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs>, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
Inline image 1
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com <mailto:aysam.guerler@gmail.com>> wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Hi Bjoern, Thanks a lot for your reply. That is the problem. That code is generated dynamically and seems a tmp file. I did not find the code which generated the tmp code. Is there a different version of MACS2 wrapper? Here is what we installed. Model-based Analysis of ChIP-Seq (macs2) stemcellcommons 642c0da30ca6 Installed toolshed.g2.bx.psu.edu The MACS14 has similar problem. Model-based Analysis of ChIP-Seq (macs2) stemcellcommons 642c0da30ca6 Installed toolshed.g2.bx.psu.edu Any idea of ngsplot? There are hard coded absolute paths in that tool? Where are those scripts in tools directory called from galaxy? Or how to change these hard coded paths to relative ones. Like tools/multiplot/multiplot.tss_tes.pl: system("/home/galaxy/galaxy-dist/tools/multiplot/multiplot.tss_tes.sh ...."). Thanks a lot. Chnagyu <javascript:void(0)> On 03/13/2014 02:14 PM, Björn Grüning wrote:
Hi,
can you point me to the MACS2 wrapper you are using? If you find the correct wrapper file you can simply replace simplejson with json and it should work.
Thanks, Bjoern
Am 13.03.2014 13:22, schrieb changyu:
Hi, I also have problems with macs and macs2 with updated galaxy. I got this error which seems a python version issue. But I can not find this file.
File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
Any suggestions?
Thanks a lot.
Changyu
Traceback (most recent call last): File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py", line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py", line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
On 3/4/14 8:01 PM, ruiwang.sz wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>"
guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1>">
<tool_shed>toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>ae2ec275332a</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1></id>
<version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>,
we could see that in this dir /home/bioinfoadmin/app/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs>, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
Inline image 1
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com <mailto:aysam.guerler@gmail.com>> wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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Hi, sorry I do not know that group/author maybe you can contact him. You will find a 'contact author' button in the toolshed. If you are brave enough you can find a MACS2 wrapper here: http://testtoolshed.g2.bx.psu.edu/view/iuc/macs2 That one is a community effort, together with Quang Trinh and Tao Liu. You are welcome to contribute fixes and enhancements. Cheers, Bjoern Am 14.03.2014 16:34, schrieb changyu_fan:
Hi Bjoern, Thanks a lot for your reply. That is the problem. That code is generated dynamically and seems a tmp file. I did not find the code which generated the tmp code.
Is there a different version of MACS2 wrapper? Here is what we installed.
Model-based Analysis of ChIP-Seq (macs2)
stemcellcommons
642c0da30ca6
Installed
toolshed.g2.bx.psu.edu
The MACS14 has similar problem.
Model-based Analysis of ChIP-Seq (macs2)
stemcellcommons
642c0da30ca6
Installed
toolshed.g2.bx.psu.edu
Any idea of ngsplot? There are hard coded absolute paths in that tool? Where are those scripts in tools directory called from galaxy? Or how to change these hard coded paths to relative ones. Like tools/multiplot/multiplot.tss_tes.pl: system("/home/galaxy/galaxy-dist/tools/multiplot/multiplot.tss_tes.sh ....").
Thanks a lot. Chnagyu
<javascript:void(0)>
On 03/13/2014 02:14 PM, Björn Grüning wrote:
Hi,
can you point me to the MACS2 wrapper you are using? If you find the correct wrapper file you can simply replace simplejson with json and it should work.
Thanks, Bjoern
Am 13.03.2014 13:22, schrieb changyu:
Hi, I also have problems with macs and macs2 with updated galaxy. I got this error which seems a python version issue. But I can not find this file.
File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
Any suggestions?
Thanks a lot.
Changyu
Traceback (most recent call last): File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py", line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py", line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
On 3/4/14 8:01 PM, ruiwang.sz wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>"
guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1>">
<tool_shed>toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>ae2ec275332a</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1 <http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1></id>
<version>1.0.1</version> </tool> </section>
if we dive in this file toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>,
we could see that in this dir /home/bioinfoadmin/app/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs>, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
Inline image 1
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
line 859, in parse tree.parse(source, parser) File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com <mailto:aysam.guerler@gmail.com>> wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi, I'm the maintainer of http://toolshed.g2.bx.psu.edu/view/stemcellcommons/macs2. It is just a fork of http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 with the following change (basically, removed the requirements section): 1c1,6 < <tool id="macs2_peakcalling" name="MACS2" version="2.0.10"> ---
<tool id="modencode_peakcalling_macs2" name="MACS2" version="2.0.10.2"> <requirements> <requirement type="python-module">macs2</requirement> <requirement type="package" version="2.0.10.2">macs2</requirement> <!--<requirement type="set_environment">SCRIPT_PATH</requirement>--> </requirements> 228c233 < </tool>
</tool> \ No newline at end of file
Ilya On 3/14/14 11:39 AM, "Björn Grüning" <bjoern.gruening@gmail.com> wrote:
Hi,
sorry I do not know that group/author maybe you can contact him. You will find a 'contact author' button in the toolshed.
If you are brave enough you can find a MACS2 wrapper here: http://testtoolshed.g2.bx.psu.edu/view/iuc/macs2
That one is a community effort, together with Quang Trinh and Tao Liu. You are welcome to contribute fixes and enhancements.
Cheers, Bjoern
Am 14.03.2014 16:34, schrieb changyu_fan:
Hi Bjoern, Thanks a lot for your reply. That is the problem. That code is generated dynamically and seems a tmp file. I did not find the code which generated the tmp code.
Is there a different version of MACS2 wrapper? Here is what we installed.
Model-based Analysis of ChIP-Seq (macs2)
stemcellcommons
642c0da30ca6
Installed
toolshed.g2.bx.psu.edu
The MACS14 has similar problem.
Model-based Analysis of ChIP-Seq (macs2)
stemcellcommons
642c0da30ca6
Installed
toolshed.g2.bx.psu.edu
Any idea of ngsplot? There are hard coded absolute paths in that tool? Where are those scripts in tools directory called from galaxy? Or how to change these hard coded paths to relative ones. Like tools/multiplot/multiplot.tss_tes.pl: system("/home/galaxy/galaxy-dist/tools/multiplot/multiplot.tss_tes.sh ....").
Thanks a lot. Chnagyu
<javascript:void(0)>
On 03/13/2014 02:14 PM, Björn Grüning wrote:
Hi,
can you point me to the MACS2 wrapper you are using? If you find the correct wrapper file you can simply replace simplejson with json and it should work.
Thanks, Bjoern
Am 13.03.2014 13:22, schrieb changyu:
Hi, I also have problems with macs and macs2 with updated galaxy. I got this error which seems a python version issue. But I can not find this file.
File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
Any suggestions?
Thanks a lot.
Changyu
Traceback (most recent call last): File
"/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jo bs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File
"/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jo bs/__init__.py", line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File
"/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/to ols/__init__.py", line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File
"/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/ut il/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File
"/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah- 2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond ImportError: No module named simplejson
On 3/4/14 8:01 PM, ruiwang.sz wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is 1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from tool_shed, things broke. In the galaxy tool panel, it looks the same like before(as expected), but when I click on macs, it will show an option of MACS 'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version=""> <tool
file="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs _wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/ma cs_wrapper.xml>"
guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0 .1>">
<tool_shed>toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu></tool_shed> <repository_name>macs</repository_name> <repository_owner>devteam</repository_owner>
<installed_changeset_revision>ae2ec275332a</installed_changeset_revisi on>
<id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0 .1></id>
<version>1.0.1</version> </tool> </section>
if we dive in this file
toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapp er.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/ma cs_wrapper.xml>,
we could see that in this dir
/home/bioinfoadmin/app/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam /macs/ae2ec275332a/macs
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs>, there is a tool_dependency xml file that has following content:
<?xml version="1.0"?> <tool_dependency> <package name="macs" version="1.3.7.1"> <repository changeset_revision="a7ea583a35d2" name="package_macs_1_3_7_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="2.15.0"> <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2). could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements> <requirement type="package" version="1.3.7.1">macs</requirement> <requirement type="package" version="2.15.0">R</requirement> </requirements>
Seems that this is the tool_shed version of macs(which is identical to the one on main galaxy server, I think?). However this one does not work with our input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs, it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that tool_shed is a cleaner way to manage tools, but in our situation the upgrade and elimination actually broke the thing that worked before. I want to ask the proper way to handle this kind of situation. could I simply drop the entry from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml entry? in that way we could continue using the 1.4.2 we have. However next time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to handle multiple version/dependency version for a tool? is there an option to not use the tool_shed but keep own version?
Thanks, Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't actually reflect tools installed in Galaxy. Please log in as an admin and check 'Manage installed tool shed repositories' menu. Try to find a tool that is installed and in tool_conf.xml but is not showing up in the tool panel. Uninstall and install this tool again. That should create entry in shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database version 118 migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading repository lib/tool_shed/galaxy_install/migrate... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository bowtie2 owned by devteam to repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie and samtools, etc. So, should I remove the corresponding entries in the tool_conf.xml? Now seems many of the tools were installed back by the toolshed but I don't see them on the panel, how to enable them? I thought this would be done by the migration script?
Thanks, Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
oh, I took that back, I think these are the tools that I installed but does not come with Galaxy. probably that's the ? means -- it is not part of the distribution?
thanks, Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks, Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
could you please try 'hg status' and tell us what it outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best, Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech <marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Hello Rui,
the process of migrating tools from Galaxy itself to the ToolShed (Galaxy's appstore) is ongoing and is well described here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it helps you with your instance.
Afterwards we can continue to troubleshoot the upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Sam,
I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u 2. ./run.sh --daemon (many error msg, follow the suggestion,then ) 3. sh manage_db.sh upgrade (update db to 118 version, start again) 4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did) 5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
Inline image 1
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml
...migrate 7->8 ...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0009_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml execute_dwt_var_perFeature.xml GMAJ.xml rgWebLogo3.xml rgClustalw.xml gi2taxonomy.xml t2t_report.xml t2ps_wrapper.xml find_diag_hits.xml lca.xml poisson2test.xml rgFastQC.xml fastq_groomer.xml fastq_paired_end_splitter.xml fastq_paired_end_joiner.xml fastq_stats.xml fastq_combiner.xml fastq_filter.xml fastq_trimmer.xml fastq_trimmer_by_quality.xml fastq_masker_by_quality.xml fastq_paired_end_interlacer.xml fastq_paired_end_deinterlacer.xml fastq_manipulation.xml fastq_to_tabular.xml tabular_to_fastq.xml bowtie2_wrapper.xml tophat_wrapper.xml tophat2_wrapper.xml express_wrapper.xml filter_transcripts_via_tracking.xml macs_wrapper.xml sicer_wrapper.xml ccat_wrapper.xml freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File
"/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py 2.7.egg/elementtree/ElementTree.py",
line 859, in parse tree.parse(source, parser) File
"/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py 2.7.egg/elementtree/ElementTree.py",
line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool tree = load_tool( config_file ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool tree = parse_xml(path) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml tree = ElementTree.parse(fname) File
"/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py 2.7.egg/elementtree/ElementTree.py",
line 859, in parse tree.parse(source, parser) File
"/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py 2.7.egg/elementtree/ElementTree.py",
line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml' IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml' IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml' IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml' IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml' IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml' IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml' IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml' IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml' IOError: [Errno 2] No such file or directory:
'./tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_G ALAXY.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml' IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml' IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml' IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml' IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml' IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml' IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml' IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml' IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks, Rui
On Thu, Feb 27, 2014 at 7:21 PM, sam guerler <aysam.guerler@gmail.com <mailto:aysam.guerler@gmail.com>> wrote:
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data' > 'Upload file from your computer'? Or the new upload dialog by clicking on 'Load Data'? Could you also please let me know if this error occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz <http://ruiwang.sz> <ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date.
Thanks! Rui
Error messages:
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
Exception happened during processing of request from (, 52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
----------------------------------------
Exception happened during processing of request from (----------------------------------------
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262----------------------------------------
)
Exception happened during processing of request from ('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1', ----------------------------------------
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste /httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.flush()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
File "/usr/lib/python2.7/socket.py", line 303, in flush
self.wfile.flush()
File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
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To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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participants (10)
-
Björn Grüning -
Björn Grüning -
changyu -
changyu_fan
-
John Chilton -
Martin Čech -
Nate Coraor -
ruiwang.sz -
sam guerler -
Sytchev, Ilya