*Hello,*
I am interested in defining vispa tool on galaxy *(http://alla.cs.gsu.edu/~software/VISPA/vispa.html).* *we usually run vispa using main.bash file as follows ./main.bash readFile referenceFile threads n t where: 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 readFile_I_2_20_CNTGS_DIST0_EM20.txt ('readFile'+'_I_2_20_CNTGS_DIST0_EM20.txt')
*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.
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 ?
*Your Help Is Highly Appreciated, Bassam Tork.* *PhD - GSU*