Follow the Galaxy wiki https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User 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 drmaa_external_runner.py file or in the galaxy admin environment profile
- Edit the drmaa_external_runner.py file to add in the LSF environment variable "BSUB_QUIET" to disable message print out. Line in blue below.
scripts/drmaa_external_runner.py:
def main():
userid, json_filename, assign_all_groups = validate_paramters()
set_user(userid, assign_all_groups)
json_file_exists(json_filename)
os.environ['BSUB_QUIET'] = 'Y'
s = drmaa.Session()
s.initialize()
jt = s.createJobTemplate()
load_job_template_from_file(jt, json_filename)
OR
- Disable LSF message in the galaxy admin profile
e.g.
export BSUB_QUIET=Y in .bash_profile
Regards,
Linda