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 That error makes me think you might be running an outdated version of galaxy code - the toolshed code has undergone extensive revision over the last few months?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 <dannonbaker@me.com>
> 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 <mtobias@wustl.edu> 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
> > <section name="Multiple Alignments" id="clustal">
> > <tool file="rgenetics/rgClustalw.xml" />
> > </section>
>
> 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 - <type 'exceptions.UnboundLocalError'>: 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_installation_required )
> UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
>
>
> CGI Variables
> -------------
> CONTENT_LENGTH: '0'
> HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
> HTTP_CONNECTION: 'Keep-Alive'
> HTTP_COOKIE: 'WUIS8102-80-PORTAL-PSJSESSIONID=vJ1cTLKhNLp82nnyBKdpQYpFZ6kXFDfy!1120331253; galaxysession=c6ca0ddb55be603a6f22339f9080446c51be220fca921cf6ad3d6a9f553baebef4e0f5ce3ecca662; __utma=87715358.305203722.1384189840.1401730273.1401811101.37; __utmc=87715358; __utmz=87715358.1395079702.27.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided); __utma=72433473.701769505.1384176472.1401971566.1402057068.268; __utmc=72433473; __utmz=72433473.1398105349.190.23.utmcsr=chpc.wustl.edu|utmccn=(referral)|utmcmd=referral|utmcct=/'
> HTTP_DNT: '1'
> HTTP_HOST: 'galaxy.chpc.wustl.edu'
> HTTP_REFERER: 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=0e5d027cf47ecae0&changeset_revision=7cc64024fe92'
> HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0'
> HTTP_X_FORWARDED_FOR: '10.28.56.101'
> HTTP_X_FORWARDED_HOST: 'galaxy.chpc.wustl.edu'
> HTTP_X_FORWARDED_SERVER: 'galaxy.chpc.wustl.edu'
> ORGINAL_HTTP_HOST: 'localhost:8082'
> ORGINAL_REMOTE_ADDR: '127.0.0.1'
> PATH_INFO: '/admin_toolshed/prepare_for_install'
> QUERY_STRING: 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92'
> REMOTE_ADDR: '10.28.56.101'
> REQUEST_METHOD: 'GET'
> SERVER_NAME: '0.0.0.0'
> SERVER_PORT: '8082'
> SERVER_PROTOCOL: 'HTTP/1.1'
>
>
> WSGI Variables
> --------------
> application: <paste.recursive.RecursiveMiddleware object at 0x19ab2990>
> is_api_request: False
> paste.cookies: (<SimpleCookie: WUIS8102-80-PORTAL-PSJSESSIONID='vJ1cTLKhNLp82nnyBKdpQYpFZ6kXFDfy!1120331253' __utma='72433473.701769505.1384176472.1401971566.1402057068.268' __utmc='72433473' __utmz='72433473.1398105349.190.23.utmcsr=chpc.wustl.edu|utmccn=(referral)|utmcmd=referral|utmcct=/' galaxysession='c6ca0ddb55be603a6f22339f9080446c51be220fca921cf6ad3d6a9f553baebef4e0f5ce3ecca662'>, 'WUIS8102-80-PORTAL-PSJSESSIONID=vJ1cTLKhNLp82nnyBKdpQYpFZ6kXFDfy!1120331253; galaxysession=c6ca0ddb55be603a6f22339f9080446c51be220fca921cf6ad3d6a9f553baebef4e0f5ce3ecca662; __utma=87715358.305203722.1384189840.1401730273.1401811101.37; __utmc=87715358; __utmz=87715358.1395079702.27.3.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided); __utma=72433473.701769505.1384176472.1401971566.1402057068.268; __utmc=72433473; __utmz=72433473.1398105349.190.23.utmcsr=chpc.wustl.edu|utmccn=(referral)|utmcmd=referral|utmcct=/')
> paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x19ab2950>
> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x2afa5c80d750>
> paste.parsed_querystring: ([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '0e5d027cf47ecae0'), ('changeset_revisions', '7cc64024fe92')], 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92')
> paste.recursive.forward: <paste.recursive.Forwarder from />
> paste.recursive.include: <paste.recursive.Includer from />
> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
> paste.recursive.script_name: ''
> paste.throw_errors: True
> request_id: '59d54a36ed7d11e387af00215ec7734c'
> webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '0e5d027cf47ecae0'), ('changeset_revisions', '7cc64024fe92')]), 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=0e5d027cf47ecae0&changeset_revisions=7cc64024fe92')
> wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
>
>
> On Thursday 05 June 2014 18:19:59 Ross wrote:
> > 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 <mtobias@wustl.edu> 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/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/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"
> > galaxy.jobs.runners DEBUG 2014-06-05 10:37:46,609 executing external set_meta script for job 779: /home/galaxy/galaxy-dist/set_metadata.sh ./database/files /home/galaxy/galaxy-dist/database/job_working_directory/000/779 . /home/galaxy/galaxy-dist/universe_wsgi.ini /home/galaxy/galaxy-dist/database/tmp/tmpsnNodx /home/galaxy/galaxy-dist/database/job_working_directory/000/779/galaxy.json /home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_in_HistoryDatasetAssociation_1448_zaFZp3,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_kwds_HistoryDatasetAssociation_1448_Rltsef,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_out_HistoryDatasetAssociation_1448_12s67j,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_results_HistoryDatasetAssociation_1448_Qucqzx,,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_override_HistoryDatasetAssociation_1448_95Vr9q /home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_in_HistoryDatasetAssociation_1447_Zh2tCn,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_kwds_HistoryDatasetAssociation_1447_UeH8AF,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_out_HistoryDatasetAssociation_1447_cZxp2H,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_results_HistoryDatasetAssociation_1447_ck1M8o,,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_override_HistoryDatasetAssociation_1447_pefoLl
> >
> >
> > --
> > Malcolm Tobias
> > 314.362.1594
> >
> >
> >
> > ___________________________________________________________
> > 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/
> >
> >
> >
> --
> Malcolm Tobias
> 314.362.1594
>
>
>
> ___________________________________________________________
> 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/
>
>
>
--
Malcolm Tobias
314.362.1594