I'd keep working on pbs_python or switch to drmaa that frequently works for the same distribution. There is also a CLI runner that just executes qsub and qstat commands directly on the localhost or can also ssh into a remote host and execute these commands.

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_... https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_...

If you must modify the wrapper to add a qsub in there - can you grab the working directory at runtime? I don't think it is actually exposed at command generation time.

CWD=`pwd`; qsub ... $CWD

Something like that, I don't know.

-John

On Tue, Sep 15, 2015 at 11:08 PM, Ryan Johnson rjohns03@carc.unm.edu wrote:

Hello all,

We are setting up a galaxy instance that will submit jobs to our cluster. We could not get pbs_python to work so we have added all PBS logic to the cheetah template wrapper ncbi_blastp_wrapper.xml.

Currently, all jobs are running out of the home directory. We want to add logic to the wrapper which will get the working directory from the JobWrapper class and then change to that directory and run from there.

Can anyone help us to access the JobWrapper.working_underscore value? Or suggest a better way to do this?

Thank you very much,

Ryan

-- Ryan S. Johnson, PhD Applications Scientist Center for Advanced Research Computing P: (650) 430-6194 E: rjohns03@carc.unm.edu

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