ClustalW jobs aren't working

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ClustalW jobs aren't working

Malcolm Tobias

 

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

 

 


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Re: ClustalW jobs aren't working

Ross-2
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 <[hidden email]> 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
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Re: ClustalW jobs aren't working

Malcolm Tobias

 

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

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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 <[hidden email]> 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

 

 


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Re: ClustalW jobs aren't working

Ross-2
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 <[hidden email]>
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 <[hidden email]> 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=/')

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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 <[hidden email]> 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"
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and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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  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
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Re: ClustalW jobs aren't working

Malcolm Tobias

 

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 <[hidden email]>

> 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 <[hidden email]> 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 <[hidden email]> 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

 

 


___________________________________________________________
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Re: ClustalW jobs aren't working

Malcolm Tobias

 

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?

 

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 <[hidden email]>

> > 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 <[hidden email]> 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 <[hidden email]> 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

 

 


___________________________________________________________
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Re: ClustalW jobs aren't working

Daniel Blankenberg
Hi Malcolm,

You’ll need to open and look at the three files that failed to merge and manually resolve the differences. See also: http://mercurial.selenic.com/wiki/TutorialConflict


You’ll want to pay attention to the 
<<<<<<< local 
and 
>>>>>>> other
lines and surrounding content to see where the conflicts occurred. 



Thanks for using Galaxy,

Dan


On Jun 9, 2014, at 1:33 PM, Malcolm Tobias <[hidden email]> 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?

 

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 <[hidden email]>
> > 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 <[hidden email]> 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
> > 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_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'
> > 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 <[hidden email]> 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:
> > >
> > > To search Galaxy mailing lists use the unified search at:
> > >
> > >
> > >
> > --
> > 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:
> >
> > To search Galaxy mailing lists use the unified search at:
> >
> >
> >
>
--
Malcolm Tobias
314.362.1594

 

 

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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___________________________________________________________
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Re: ClustalW jobs aren't working

Hans-Rudolf Hotz
In reply to this post by Malcolm Tobias


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 <[hidden email]>
>
>  > > 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 <[hidden email]>
> 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
> <[hidden email]> 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
>
>
>
> ___________________________________________________________
> 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/
>
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>
___________________________________________________________
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Re: ClustalW jobs aren't working

Malcolm Tobias

 

All,

 

After updating to the latest/greatest Galaxy, I was able to install ClustalW from the tool shed and everything appears to be working as expected.

 

Thanks for everyone's help in resolving this.

 

Cheers,

Malcolm

 

On Tuesday 10 June 2014 01:43:59 Hans-Rudolf Hotz wrote:

>

> 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 <[hidden email]>

> >

> > > > 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 <[hidden email]>

> > 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:

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> > __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

> > <[hidden email]> 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

> >

> >

> >

> > ___________________________________________________________

> > 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

 

 


___________________________________________________________
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