[galaxy-dev] defining genome assembler in galaxy

[Bassam Tork]

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 at 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.
>
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