From 71891839e397130fb1af3e499d30fa9a953a93f7 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 18 Feb 2022 15:47:46 +0100 Subject: [PATCH] fix: do not pass SNAKEMAKE_PROFILE into cluster-submit (#1398) (#1407) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * feat: cluster sidecar * fix: do not pass SNAKEMAKE_PROFILE into cluster-submit (#1398) Co-authored-by: Johannes Köster --- snakemake/executors/__init__.py | 5 +++++ tests/test_cluster_statusscript/qsub | 4 ++++ 2 files changed, 9 insertions(+) diff --git a/snakemake/executors/__init__.py b/snakemake/executors/__init__.py index d8628d2fa..8fe0ebb96 100644 --- a/snakemake/executors/__init__.py +++ b/snakemake/executors/__init__.py @@ -1130,6 +1130,11 @@ def run(self, job, callback=None, submit_callback=None, error_callback=None): env = dict(os.environ) if self.sidecar_vars: env["SNAKEMAKE_CLUSTER_SIDECAR_VARS"] = self.sidecar_vars + + # Remove SNAKEMAKE_PROFILE from environment as the snakemake call inside + # of the cluster job must run locally (or complains about missing -j). + env.pop("SNAKEMAKE_PROFILE", None) + ext_jobid = ( subprocess.check_output( '{submitcmd} "{jobscript}"'.format( diff --git a/tests/test_cluster_statusscript/qsub b/tests/test_cluster_statusscript/qsub index 0bc8aabba..5857ca5f0 100755 --- a/tests/test_cluster_statusscript/qsub +++ b/tests/test_cluster_statusscript/qsub @@ -1,4 +1,8 @@ #!/bin/bash +if [[ ! -z "$SNAKEMAKE_PROFILE" ]]; then + >&2 echo "SNAKEMAKE_PROFILE should not be set" + exit 1 +fi echo `date` >> qsub.log tail -n1 $1 >> qsub.log # simulate printing of job id by a random number