fix: do not pass SNAKEMAKE_PROFILE into cluster-submit (#1398)

snakemake · Feb 17, 2022 · 2488c1f · 2488c1f
1 parent 0593de1
commit 2488c1f
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diff --git a/snakemake/executors/__init__.py b/snakemake/executors/__init__.py
@@ -1070,12 +1070,17 @@ def run(self, job, callback=None, submit_callback=None, error_callback=None):
             raise WorkflowError(str(e), rule=job.rule if not job.is_group() else None)
 
         try:
+            # Remove SNAKEMAKE_PROFILE from environment as the snakemake call inside
+            # of the cluster job must run locally (or complains about missing -j).
+            env = dict(os.environ.items())
+            env.pop("SNAKEMAKE_PROFILE", None)
             ext_jobid = (
                 subprocess.check_output(
                     '{submitcmd} "{jobscript}"'.format(
                         submitcmd=submitcmd, jobscript=jobscript
                     ),
                     shell=True,
+                    env=env,
                 )
                 .decode()
                 .split("\n")

diff --git 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