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/ >> > >
