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.
https://github.com/PlatformLSF/lsf-drmaa
Level commit e4d5c1ab10fcba572eaede68fc2fc05332198bec or above
This fixes the LSF job id not found issue.
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___________________________________________________________
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