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/ >
