> My idea was to pass all above including main.bash as parameters to the
> python wrapper (called run.py, attached), as follows:
>
> where the last parameter sys.argv[7] is the output file, specified by xml
> file.
This is the correct approach.
> But galaxy was running for more than 3 hours, although it should take
> only 7-10 minutes on our server with no results.
>
> Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt
> , where dataset_192 .txt is the reads file.But
> dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in
> galaxy-dist/database/files/000.
> run.py: simply coppies data from dataset_192_I_2_20_CNTGS_DIST0_EM20.txt to
> galaxy output file, but nothing is coppied since
> dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created.
>
> How could the results appear?Could somebody help me ?
>
The first thing to check is if run.py functions correctly outside of Galaxy. If
so, try checking the job manually using top/qstat/similar system utilities to
figure out where the job is stuck.
Good luck,
J.
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