Re: [galaxy-dev] ClustalW jobs aren't working
On 06/09/2014 07:33 PM, Malcolm Tobias wrote: All, I apologize for an off-topic question, by my update failed: [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg pull -u | tee hg.pull.out ... added 3716 changesets with 9929 changes to 2124 files (+46 heads) ... merging lib/galaxy/app.py merging lib/galaxy/app.py failed! warning: conflicts during merge. merging lib/galaxy/model/__init__.py merging lib/galaxy/model/__init__.py failed! warning: conflicts during merge. merging lib/galaxy/model/mapping.py merging lib/galaxy/model/mapping.py failed! merging tool-data/shared/ucsc/ucsc_build_sites.txt and tool-data/shared/ucsc/ucsc_build_sites.txt.sample to tool-data/shared/ucsc/ucsc_build_sites.txt.sample 1528 files updated, 1 files merged, 1289 files removed, 3 files unresolved use 'hg resolve' to retry unresolved file merges resolve apparently can't fix this issue: [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg resolve --all merging lib/galaxy/app.py warning: conflicts during merge. merging lib/galaxy/app.py failed! merging lib/galaxy/model/__init__.py warning: conflicts during merge. merging lib/galaxy/model/__init__.py failed! merging lib/galaxy/model/mapping.py warning: conflicts during merge. merging lib/galaxy/model/mapping.py failed! What's the recommended way to fix this? Depending on your local customization, it is not unusual to get unresolved files. Open the files in an editor and complete the merge manually. Regards, Hans-Rudolf Thanks! Malcolm On Monday 09 June 2014 10:47:04 Malcolm Tobias wrote: > > Ross, > > Thanks for the response. My instance of Galaxy is indeed ancient: > > [galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg tip > changeset: 10003:b4a373d86c51 > tag: tip > parent: 10001:471484ff8be6 > user: greg > date: Wed Jun 12 11:48:09 2013 -0400 > summary: Add targets to Repository Actions menu items. > > Previous attempts at updating have been pretty painful. I'll give it a shot and let you know whether or not this fixes the problem. > > Cheers, > Malcolm > > On Friday 06 June 2014 18:30:01 Ross wrote: > > Hi Malcolm, > > That error makes me think you might be running an outdated version of galaxy code - the toolshed code has undergone extensive revision over the last few months? > > I just tested that repository on a freshly updated galaxy-central clone and it installed without drama, so I wonder what: > > > > hg tip > > > > shows? > > > > I just tested using : > > (vgalaxy)rlazarus@rlazarus-UX31A:~/galaxy$ hg tip > > changeset: 13756:84a00e4f7d06 > > tag: tip > > user:Dannon Baker > > date:Fri Jun 06 17:12:30 2014 -0400 > > summary: Clarify language in DeleteIntermediateDataset PJA. > > > > If your clone is not up to date, I'd recommend completely removing the failed installation (through the admin menu - check the box for complete removal), shut down galaxy, backup your database, do the usual hg pull -u dance and any necessary database upgrade steps then try a clean install? > > > > Thanks for reporting this - if it persists on recent Galaxy code we'll need to do some deeper investigation. > > > > > > On Fri, Jun 6, 2014 at 11:32 PM, Malcolm Tobias wrote: > > > > Ross, > > > > Thanks for the reply! Unfortunately I am the local Galaxy admin ;-) > > > > I had tried installing the clustalw tool from the toolshed, but that failed with an error (more on that later). I disabled the local tool: > > > > [galaxy@login002 galaxy-dist]$ diff tool_conf.xml tool_conf.xml.bkup > > 226a227,229 > > > > > > > > > > > > > bounced galaxy in case that's necessary, then retried installing from the toolshed. Shortly after clicking install, I get this message: > > > > Internal Server Error > > Galaxy was unable to sucessfully complete your request > > > > An error occurred. > > This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. > > > > The error has been logged to our team. > > > > The logs appear to be complaining about 'prior_installation_required' which I'm assuming means the package_clustalw_2_1 dependency. I was able to install that, and I can verify by looking at the local toolshed: > > > > [galaxy@login002 ~]$ ls galaxy-toolshed/toolshed.g2.bx.psu.edu/repos/devteam/ > > bowtie_wrappers package_clustalw_2_1 package_vcftools_0_1_11 > > bwa_wrappers package_fastx_toolkit_0_0_13 > > > > Again, I'll post the logs from when the install fails in case that helps. Any suggestions are much appreciated. > > > > Cheers, > > Malcolm > > > > > > 10.28.56.101 - - [06/Jun/2014:08:20:38 -0500] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92 HTTP/1.1" 500 - "http://toolshed.g2.bx
Re: [galaxy-dev] ClustalW jobs aren't working
Hi Malcolm, That error makes me think you might be running an outdated version of galaxy code - the toolshed code has undergone extensive revision over the last few months? I just tested that repository on a freshly updated galaxy-central clone and it installed without drama, so I wonder what: hg tip shows? I just tested using : (vgalaxy)rlazarus@rlazarus-UX31A:~/galaxy$ hg tip changeset: 13756:84a00e4f7d06 tag: tip user:Dannon Baker date:Fri Jun 06 17:12:30 2014 -0400 summary: Clarify language in DeleteIntermediateDataset PJA. If your clone is not up to date, I'd recommend completely removing the failed installation (through the admin menu - check the box for complete removal), shut down galaxy, backup your database, do the usual hg pull -u dance and any necessary database upgrade steps then try a clean install? Thanks for reporting this - if it persists on recent Galaxy code we'll need to do some deeper investigation. On Fri, Jun 6, 2014 at 11:32 PM, Malcolm Tobias wrote: > > > Ross, > > > > Thanks for the reply! Unfortunately I am the local Galaxy admin ;-) > > > > I had tried installing the clustalw tool from the toolshed, but that > failed with an error (more on that later). I disabled the local tool: > > > > [galaxy@login002 galaxy-dist]$ diff tool_conf.xml tool_conf.xml.bkup > > 226a227,229 > > > > > > > > > > > > > bounced galaxy in case that's necessary, then retried installing from the > toolshed. Shortly after clicking install, I get this message: > > > > Internal Server Error > > Galaxy was unable to sucessfully complete your request > > > > An error occurred. > > This may be an intermittent problem due to load or other unpredictable > factors, reloading the page may address the problem. > > > > The error has been logged to our team. > > > > The logs appear to be complaining about 'prior_installation_required' > which I'm assuming means the package_clustalw_2_1 dependency. I was able to > install that, and I can verify by looking at the local toolshed: > > > > [galaxy@login002 ~]$ ls galaxy-toolshed/ > toolshed.g2.bx.psu.edu/repos/devteam/ > > bowtie_wrappers package_clustalw_2_1 package_vcftools_0_1_11 > > bwa_wrappers package_fastx_toolkit_0_0_13 > > > > Again, I'll post the logs from when the install fails in case that helps. > Any suggestions are much appreciated. > > > > Cheers, > > Malcolm > > > > > > 10.28.56.101 - - [06/Jun/2014:08:20:38 -0500] "GET > /admin_toolshed/prepare_for_install?tool_shed_url= > http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92 > HTTP/1.1" 500 - " > http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=0e5d027cf47ecae0&changeset_revision=7cc64024fe92"; > "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" > > Error - : local variable > 'prior_installation_required' referenced before assignment > > URL: > http://galaxy.chpc.wustl.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92 > > File > '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', > line 149 in __call__ > > app_iter = self.application(environ, sr_checker) > > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > > return self.application(environ, start_response) > > File > '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > > return self.application(environ, start_response) > > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 > in __call__ > > return self.handle_request( environ, start_response ) > > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 > in handle_request > > body = method( trans, **kwargs ) > > File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > 221 in decorator > > return func( self, trans, *args, **kwargs ) > > File > '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', > line 896 in prepare_for_install > > common_install_util.get_dependencies_for_repository( trans, tool_shed_url, > repo_info_dict, includes_tool_dependencies ) > > File '/home/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', > line 84 in get_dependencies_for_repository > > installed_rd, missing_rd = > get_installed_and_missing_repository_dependencies_for_new_install( trans, > repo_info_tuple ) > > File '/home/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', > line 190 in > get_installed_and_missing_repository_dependencies_for_new_install > > tool_shed, name, owner, changeset_revision, prior_installation_required = > suc.parse_repository_dependency_tuple( rd_tup ) > > File '/home/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py', > line 1132 in parse_repository_dependency_tuple > > prior_installation_required = str( prior_in
Re: [galaxy-dev] ClustalW jobs aren't working
Malcolm, It looks like you have downloaded the wrapper and put it in your local tools folder. We strongly recommend that you remove the tool_conf.xml entry and get the local galaxy administrator to install the devteam clustalw repository from the main toolshed. That should solve your problem - please let us know if not. You can browse that repo here http://toolshed.g2.bx.psu.edu/view/devteam/clustalw and install it from the admin menu; search and browse tool sheds; main tool shed;... On Fri, Jun 6, 2014 at 3:24 AM, Malcolm Tobias wrote: > > > All, > > > > When running clustalW jobs, the only output we're getting is an error > message that appears to show the tool isn't receiving the proper run-time > parameters: > > > > > > Unknown option: I > > Value "FILE=infile_copy" invalid for option N (number expected) > > Unknown option: F > > Unknown option: I > > Unknown option: L > > Unknown option: E > > ... > > > This appears to come from the rgClustalw.py wrapper: > > > cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s > -OUTPUT=%s > > ' % > (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts. > > outform)] > > > > > Strangely, the log files appear to show the correct paramters: > > > galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency on > 'clustalw2', ignoring > > galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing: > python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i > "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o > "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" > -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t > "Clustal_run" -d "DNA" -f "CLUSTAL" > > > > I'll post the full output from the logs below, but I was hoping someone > might be able to offer some suggestions on how to debug this further. > > > > Thanks! > > Malcolm > > > > 10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "POST /tool_runner/index > HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/tool_runner?tool_id=clustalw"; > "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" > > galaxy.jobs DEBUG 2014-06-05 10:37:43,025 (779) Working directory for job > is: /home/galaxy/galaxy-dist/database/job_working_directory/000/779 > > galaxy.jobs.handler DEBUG 2014-06-05 10:37:43,057 (779) Dispatching to > local runner > > galaxy.jobs DEBUG 2014-06-05 10:37:43,205 (779) Persisting job > destination (destination id: local) > > galaxy.jobs.handler INFO 2014-06-05 10:37:43,258 (779) Job dispatched > > 10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "GET /history HTTP/1.1" 200 > - "http://galaxy.chpc.wustl.edu/tool_runner/index"; "Mozilla/5.0 (X11; > Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" > > galaxy.tools DEBUG 2014-06-05 10:37:43,466 Building dependency shell > command for dependency 'clustalw2' > > galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency > on 'clustalw2', ignoring > > galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing: > python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i > "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o > "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" > -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t > "Clustal_run" -d "DNA" -f "CLUSTAL" > > 10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET > /api/histories/1ac3b66e11b8fe50 HTTP/1.1" 200 - " > http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64; > rv:24.0) Gecko/20100101 Firefox/24.0" > > galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,732 Exception caught > attempting to generate viewport for dataset '972' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line > 159, in get_estimated_display_viewport > > fh = open( dataset.file_name ) > > IOError: [Errno 2] No such file or directory: > '/home/galaxy/galaxy-dist/database/files/000/dataset_769.dat' > > galaxy.jobs DEBUG 2014-06-05 10:37:43,736 (779) Persisting job > destination (destination id: local) > > galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,776 Exception caught > attempting to generate viewport for dataset '985' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line > 159, in get_estimated_display_viewport > > fh = open( dataset.file_name ) > > IOError: [Errno 2] No such file or directory: > '/home/galaxy/galaxy-dist/database/files/000/dataset_782.dat' > > galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,830 Exception caught > attempting to generate viewport for dataset '986' > > Traceback (most recent call last): > > File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line > 159, in get_estimated_display_viewport > > fh = open( dataset.file_name ) > > IOError: [Errno 2] No such file or directory: > '/home/galaxy/galaxy-dist/databas
[galaxy-dev] ClustalW jobs aren't working
All, When running clustalW jobs, the only output we're getting is an error message that appears to show the tool isn't receiving the proper run-time parameters: Unknown option: I Value "FILE=infile_copy" invalid for option N (number expected) Unknown option: F Unknown option: I Unknown option: L Unknown option: E ... This appears to come from the rgClustalw.py wrapper: cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s -OUTPUT=%s ' % (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts. outform)] Strangely, the log files appear to show the correct paramters: galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency on 'clustalw2', ignoring galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL" I'll post the full output from the logs below, but I was hoping someone might be able to offer some suggestions on how to debug this further. Thanks! Malcolm 10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/tool_runner?tool_id=clustalw"; "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" galaxy.jobs DEBUG 2014-06-05 10:37:43,025 (779) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/779 galaxy.jobs.handler DEBUG 2014-06-05 10:37:43,057 (779) Dispatching to local runner galaxy.jobs DEBUG 2014-06-05 10:37:43,205 (779) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2014-06-05 10:37:43,258 (779) Job dispatched 10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "GET /history HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/tool_runner/index"; "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" galaxy.tools DEBUG 2014-06-05 10:37:43,466 Building dependency shell command for dependency 'clustalw2' galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency on 'clustalw2', ignoring galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED" -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL" 10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET /api/histories/1ac3b66e11b8fe50 HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,732 Exception caught attempting to generate viewport for dataset '972' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159, in get_estimated_display_viewport fh = open( dataset.file_name ) IOError: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/files/000/dataset_769.dat' galaxy.jobs DEBUG 2014-06-05 10:37:43,736 (779) Persisting job destination (destination id: local) galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,776 Exception caught attempting to generate viewport for dataset '985' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159, in get_estimated_display_viewport fh = open( dataset.file_name ) IOError: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/files/000/dataset_782.dat' galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,830 Exception caught attempting to generate viewport for dataset '986' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159, in get_estimated_display_viewport fh = open( dataset.file_name ) IOError: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/files/000/dataset_783.dat' galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,876 Exception caught attempting to generate viewport for dataset '987' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line 159, in get_estimated_display_viewport fh = open( dataset.file_name ) IOError: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/files/000/dataset_784.dat' 10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET /history/get_display_application_links HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:45,983 execution finished: python /home/galaxy/galaxy-dist/tools/rgene
