Merge pull request #327 from mskcc/master

Master to Develop
mskcc · Oct 13, 2023 · 4210256 · 4210256
2 parents a6ce99f + ab7efb1
commit 4210256
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/batch_systems/lsf_client/lsf_client.py b/batch_systems/lsf_client/lsf_client.py
@@ -42,7 +42,10 @@ def submit(self, command, job_args, stdout, job_id, env={}):
         Returns:
             int: lsf job id
         """
-        bsub_command = ["bsub", "-sla", settings.LSF_SLA, "-g", format_lsf_job_id(job_id), "-oo", stdout] + job_args
+        if settings.LSF_SLA:
+            bsub_command = ["bsub", "-sla", settings.LSF_SLA, "-g", format_lsf_job_id(job_id), "-oo", stdout] + job_args
+        else:
+            bsub_command = ["bsub", "-g", format_lsf_job_id(job_id), "-oo", stdout] + job_args
 
         bsub_command.extend(command)
         current_env = os.environ.copy()

diff --git a/ridgeback/settings.py b/ridgeback/settings.py
@@ -247,7 +247,7 @@
 TOIL_WORK_DIR_ROOT = os.environ["RIDGEBACK_TOIL_WORK_DIR_ROOT"]
 TOIL_TMP_DIR_ROOT = os.environ["RIDGEBACK_TOIL_TMP_DIR_ROOT"]
 LSF_WALLTIME = os.environ["RIDGEBACK_LSF_WALLTIME"]
-LSF_SLA = os.environ["RIDGEBACK_LSF_SLA"]
+LSF_SLA = os.environ.get("RIDGEBACK_LSF_SLA", None)
 CWLTOIL = os.environ.get("RIDGEBACK_TOIL", "toil-cwl-runner")
 TOIL_STATE_POLLING_WAIT = os.environ.get("TOIL_STATE_POLLING_WAIT", 60)
 

diff --git a/submitter/toil_submitter/toil_jobsubmitter.py b/submitter/toil_submitter/toil_jobsubmitter.py
@@ -41,7 +41,14 @@ def submit(self):
         command_line = self._command_line()
         log_path = os.path.join(self.job_work_dir, "lsf.log")
         env = dict()
-        toil_lsf_args = "-sla %s %s %s" % (settings.LSF_SLA, " ".join(self._job_group()), " ".join(self._job_args()))
+        if settings.LSF_SLA:
+            toil_lsf_args = "-sla %s %s %s" % (
+                settings.LSF_SLA,
+                " ".join(self._job_group()),
+                " ".join(self._job_args()),
+            )
+        else:
+            toil_lsf_args = "%s %s" % (" ".join(self._job_group()), " ".join(self._job_args()))
         env["JAVA_HOME"] = None
         env["TOIL_LSF_ARGS"] = toil_lsf_args
         external_id = self.lsf_client.submit(command_line, self._job_args(), log_path, self.job_id, env)