Re: Cluster jobs running as real user

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Re: Cluster jobs running as real user

Linda Cham

Follow the Galaxy wiki  setup permission instructions.

Follow these 2 steps to get Galaxy to run as real users with IBM Platform LSF:

Step 1) Download the latest LSF DRMAA 1.1.1 from github.

Step 2) LSF needs to disable message being printed out via the LSF environment variable "BSUB_QUIET". This can be done either in in Galaxy file or in the galaxy admin environment profile
  • Edit the file to add in the LSF environment variable  "BSUB_QUIET" to disable message print out.  Line in blue below.

    def main():
        userid, json_filename, assign_all_groups = validate_paramters()
        set_user(userid, assign_all_groups)
        os.environ['BSUB_QUIET'] = 'Y'
        s = drmaa.Session()
        jt = s.createJobTemplate()
        load_job_template_from_file(jt, json_filename)

  • Disable LSF message in the galaxy admin profile

     export BSUB_QUIET=Y in .bash_profile


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