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

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