Re: [galaxy-dev] defining genome assembler in galaxy
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.goe...@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. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] defining genome assembler in galaxy
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.goe...@emory.eduwrote: 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. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] 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* ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/