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ssadedin / bpipe

Bpipe - a tool for running and managing bioinformatics pipelines
http://docs.bpipe.org/
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Support for PBS Professional #82

Open lonsbio opened 10 years ago

lonsbio commented 10 years ago

From davide.r...@gmail.com on 2013-09-10T02:06:46Z

Hi, I managed to modify the bpipe-torque.sh in order to use bpipe on PBS professional.

I have made 2 major changes:

  1. line 194: qstat_output=qstat -x -f "$1"

because you need to use the -x option to ask for fonoshed jobs on pbs professional

  1. lines 210-214

added a case for "F" (status finished in PBS professional) and a different awk (with Exit_status instead of exit_status)

Especially the first change will break the PBS TORQUE support (qstat torque don't have the -x option). Which is the best way to proceeed? May be you can add another executor="pbspro" with a different sh script? (can be for example bpipe-pbspro.sh)

diff in attachment.

Best regards,

Davide Rambaldi

Attachment: torque.diff

Original issue: http://code.google.com/p/bpipe/issues/detail?id=82

lonsbio commented 10 years ago

From davide.r...@gmail.com on 2013-09-17T08:09:35Z

I am working on a fork of bpipe to add support for PBS professional: https://github.com/tucano/bpipe It contains:

  1. bin/bpipe-pbspro.sh (custom sh script for pbspro)
  2. src/main/groovy/bpipe/executor/PbsproCommandExecutor.groovy (custom command executor wrapper)

Once properly tested I will send you a pull request if you want.

Regards

Davide Rambaldi

lonsbio commented 10 years ago

From ssade...@gmail.com on 2013-09-29T05:11:07Z

Thanks for your effort on this - I will have a look at integrating it into our next version!

lonsbio commented 10 years ago

From davide.r...@gmail.com on 2013-10-08T07:40:55Z

Ok, in the meantime I will keep updated the code:

check here the status: https://github.com/tucano/bpipe/network P.S: googlecode is shutting down soon, are you moving to github?

Regards

Davide R.