> 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,
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