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 <mtob...@wustl.edu> wrote:

>
>
> All,
>
>
>
> When running clustalW jobs, the only output we're getting is an error
> message that appears to show the tool isn't receiving the proper run-time
> parameters:
>
>
>
>
>
> Unknown option: I
>
>  Value "FILE=infile_copy" invalid for option N (number expected)
>
>  Unknown option: F
>
>  Unknown option: I
>
>  Unknown option: L
>
>  Unknown option: E
>
> ...
>
>
> This appears to come from the rgClustalw.py wrapper:
>
>
>         cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s 
> -OUTPUT=%s
>
> ' %
> (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts.
>
> outform)]
>
>
>
>
> Strangely, the log files appear to show the correct paramters:
>
>
> galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency on 
> 'clustalw2', ignoring
>
> galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing:
> python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i
> "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o
> "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED"
> -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t
> "Clustal_run" -d "DNA" -f "CLUSTAL"
>
>
>
> I'll post the full output from the logs below, but I was hoping someone
> might be able to offer some suggestions on how to debug this further.
>
>
>
> Thanks!
>
> Malcolm
>
>
>
> 10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "POST /tool_runner/index
> HTTP/1.1" 200 - "http://galaxy.chpc.wustl.edu/tool_runner?tool_id=clustalw";
> "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
>
> galaxy.jobs DEBUG 2014-06-05 10:37:43,025 (779) Working directory for job
> is: /home/galaxy/galaxy-dist/database/job_working_directory/000/779
>
> galaxy.jobs.handler DEBUG 2014-06-05 10:37:43,057 (779) Dispatching to
> local runner
>
> galaxy.jobs DEBUG 2014-06-05 10:37:43,205 (779) Persisting job
> destination (destination id: local)
>
> galaxy.jobs.handler INFO 2014-06-05 10:37:43,258 (779) Job dispatched
>
> 10.28.56.101 - - [05/Jun/2014:10:37:42 -0500] "GET /history HTTP/1.1" 200
> - "http://galaxy.chpc.wustl.edu/tool_runner/index"; "Mozilla/5.0 (X11;
> Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
>
> galaxy.tools DEBUG 2014-06-05 10:37:43,466 Building dependency shell
> command for dependency 'clustalw2'
>
> galaxy.tools WARNING 2014-06-05 10:37:43,484 Failed to resolve dependency
> on 'clustalw2', ignoring
>
> galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:43,596 (779) executing:
> python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i
> "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o
> "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED"
> -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t
> "Clustal_run" -d "DNA" -f "CLUSTAL"
>
> 10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET
> /api/histories/1ac3b66e11b8fe50 HTTP/1.1" 200 - "
> http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64;
> rv:24.0) Gecko/20100101 Firefox/24.0"
>
> galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,732 Exception caught
> attempting to generate viewport for dataset '972'
>
> Traceback (most recent call last):
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line
> 159, in get_estimated_display_viewport
>
> fh = open( dataset.file_name )
>
> IOError: [Errno 2] No such file or directory:
> '/home/galaxy/galaxy-dist/database/files/000/dataset_769.dat'
>
> galaxy.jobs DEBUG 2014-06-05 10:37:43,736 (779) Persisting job
> destination (destination id: local)
>
> galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,776 Exception caught
> attempting to generate viewport for dataset '985'
>
> Traceback (most recent call last):
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line
> 159, in get_estimated_display_viewport
>
> fh = open( dataset.file_name )
>
> IOError: [Errno 2] No such file or directory:
> '/home/galaxy/galaxy-dist/database/files/000/dataset_782.dat'
>
> galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,830 Exception caught
> attempting to generate viewport for dataset '986'
>
> Traceback (most recent call last):
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line
> 159, in get_estimated_display_viewport
>
> fh = open( dataset.file_name )
>
> IOError: [Errno 2] No such file or directory:
> '/home/galaxy/galaxy-dist/database/files/000/dataset_783.dat'
>
> galaxy.datatypes.interval ERROR 2014-06-05 10:37:43,876 Exception caught
> attempting to generate viewport for dataset '987'
>
> Traceback (most recent call last):
>
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/interval.py", line
> 159, in get_estimated_display_viewport
>
> fh = open( dataset.file_name )
>
> IOError: [Errno 2] No such file or directory:
> '/home/galaxy/galaxy-dist/database/files/000/dataset_784.dat'
>
> 10.28.56.101 - - [05/Jun/2014:10:37:43 -0500] "GET
> /history/get_display_application_links HTTP/1.1" 200 - "
> http://galaxy.chpc.wustl.edu/history"; "Mozilla/5.0 (X11; Linux x86_64;
> rv:24.0) Gecko/20100101 Firefox/24.0"
>
> galaxy.jobs.runners.local DEBUG 2014-06-05 10:37:45,983 execution
> finished: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i
> "/home/galaxy/galaxy-dist/database/files/001/dataset_1243.dat" -o
> "/home/galaxy/galaxy-dist/database/files/001/dataset_1244.dat" -s "ALIGNED"
> -l "/home/galaxy/galaxy-dist/database/files/001/dataset_1245.dat" -t
> "Clustal_run" -d "DNA" -f "CLUSTAL"
>
> galaxy.jobs.runners DEBUG 2014-06-05 10:37:46,609 executing external
> set_meta script for job 779: /home/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /home/galaxy/galaxy-dist/database/job_working_directory/000/779 .
> /home/galaxy/galaxy-dist/universe_wsgi.ini
> /home/galaxy/galaxy-dist/database/tmp/tmpsnNodx
> /home/galaxy/galaxy-dist/database/job_working_directory/000/779/galaxy.json
> /home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_in_HistoryDatasetAssociation_1448_zaFZp3,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_kwds_HistoryDatasetAssociation_1448_Rltsef,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_out_HistoryDatasetAssociation_1448_12s67j,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_results_HistoryDatasetAssociation_1448_Qucqzx,,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_override_HistoryDatasetAssociation_1448_95Vr9q
> /home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_in_HistoryDatasetAssociation_1447_Zh2tCn,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_kwds_HistoryDatasetAssociation_1447_UeH8AF,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_out_HistoryDatasetAssociation_1447_cZxp2H,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_results_HistoryDatasetAssociation_1447_ck1M8o,,/home/galaxy/galaxy-dist/database/job_working_directory/000/779/metadata_override_HistoryDatasetAssociation_1447_pefoLl
>
>
>
>
> --
>
> Malcolm Tobias
>
> 314.362.1594
>
>
>
>
>
> ___________________________________________________________
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