1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e66936a92feb/ Changeset: e66936a92feb User: jmchilton Date: 2014-08-18 14:43:37 Summary: Fix for running LSF DRMAA jobs as 'real' user. Fix thanks to Chong Chen at IBM - "When invoking the LSF drmma api to submit a job, the API will print the message like 'Job <78> is submitted to default queue <normal>'. So if the Galaxy want to use this API, need modify the drmaa_external_runner.py script to handle this message. LSF already support a env variable to disable this message print out, "BSUB_QUIET", set this into env can disable this message output." A second issue was related to subsequent querying of the job state as a user other than the submitter - according to Chong Chen this has been fixed in latest LSF DRMAA changes on github (https://github.com/PlatformLSF/lsf-drmaa/commit/43e62546172b90d9f95e90273d77...). Affected #: 1 file diff -r 572a8d5ee218aeb37f77660948cb75a439936868 -r e66936a92febf952017586742db36ed44be4d08b scripts/drmaa_external_runner.py --- a/scripts/drmaa_external_runner.py +++ b/scripts/drmaa_external_runner.py @@ -124,6 +124,9 @@ userid, json_filename, assign_all_groups = validate_paramters() set_user(userid, assign_all_groups) json_file_exists(json_filename) + # Added to disable LSF generated messages that would interfer with this + # script. Fix thank to Chong Chen at IBM. + os.environ['BSUB_QUIET'] = 'Y' s = drmaa.Session() s.initialize() jt = s.createJobTemplate() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.