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/ >>> >> >> >
