defining genome assembler in galaxy
*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*
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.
Dear Jeremy, Thank You very much, I will try your suggestion. Could you please guide me to the link/webpage that talks about checking the job manually using top/qstat/similar. Happy New Year, Bassam Tork. On Thu, Dec 29, 2011 at 9:18 AM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:
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.
Top and qstat are generic unix utilities for tracking jobs. Running 'man <command>' will, assuming they are installed on your system, provide the best information for using them. J. On Dec 29, 2011, at 12:09 PM, Bassam Tork wrote:
Dear Jeremy, Thank You very much, I will try your suggestion. Could you please guide me to the link/webpage that talks about checking the job manually using top/qstat/similar. Happy New Year, Bassam Tork.
On Thu, Dec 29, 2011 at 9:18 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
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.
participants (2)
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Bassam Tork -
Jeremy Goecks