From 6117d0cbe3d2a0c7b273a681ede7cdf117415346 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 17 Feb 2021 22:15:29 +0100 Subject: [PATCH] fix slurm runner for real user setups for finished jobs (state DONE) the SLURM runner modifies the job's stderr file. for real user setups this does not work because the job dir is still owned by the real user. solution just add a reclaim ownnership before writing --- lib/galaxy/jobs/runners/slurm.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/jobs/runners/slurm.py b/lib/galaxy/jobs/runners/slurm.py index 446319df3d5..ac1f6d62bb8 100644 --- a/lib/galaxy/jobs/runners/slurm.py +++ b/lib/galaxy/jobs/runners/slurm.py @@ -153,6 +153,7 @@ class SlurmJobRunner(DRMAAJobRunner): self.work_queue.put((self.fail_job, ajs)) return if drmaa_state == self.drmaa_job_states.DONE: + ajs.job_wrapper.reclaim_ownership() with open(ajs.error_file) as rfh: _remove_spurious_top_lines(rfh, ajs) with open(ajs.error_file, 'r+') as f: