I am interested in defining vispa tool on galaxy
*we usually run vispa using main.bash file as follows
./main.bash   readFile   referenceFile  threads  n  t
threads: number of threads
n:number of mismatches
t:mutation rate
the output file name,we are interested in is not passed as parameter,
but its named as follows:
if inupt file name= readFile.fas then output file name is

*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

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
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 ?

*Your Help Is Highly Appreciated,
Bassam Tork.*
*PhD - GSU*
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