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_advanced#L22
https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L399

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 <rjohn...@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: rjohn...@carc.unm.edu
>
>
>
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