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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