From 9eeecfbdc06143d5c9f37fc1894ee22db51b7a18 Mon Sep 17 00:00:00 2001 From: nsheff Date: Fri, 24 Jul 2020 21:32:35 -0400 Subject: [PATCH 1/2] Use bash for submission --- looper/conductor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/looper/conductor.py b/looper/conductor.py index f45024941..f0880e83d 100644 --- a/looper/conductor.py +++ b/looper/conductor.py @@ -247,7 +247,7 @@ def submit(self, force=False): # Capture submission command return value so that we can # intercept and report basic submission failures; #167 try: - subprocess.check_call(submission_command, shell=True) + subprocess.check_call(submission_command, shell=True, executable="/bin/bash") except subprocess.CalledProcessError: fails = "" if self.collate \ else [s.sample_name for s in self._samples] From b5acd51ae88c9510cd28965395abe6e4ade6114f Mon Sep 17 00:00:00 2001 From: nsheff Date: Mon, 24 Apr 2023 16:36:27 -0400 Subject: [PATCH 2/2] execute submission scripts directly --- looper/conductor.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/looper/conductor.py b/looper/conductor.py index c4157ffd0..215fe3b46 100644 --- a/looper/conductor.py +++ b/looper/conductor.py @@ -522,11 +522,17 @@ def submit(self, force=False): _LOGGER.info("Dry run, not submitted") elif self._rendered_ok: sub_cmd = self.prj.dcc.compute.submission_command - submission_command = "{} {}".format(sub_cmd, script) + submission_command = f"{sub_cmd} {script}" # old way + if sub_cmd == ".": + sub_cmd_list = [script] + else: + sub_cmd_list = [sub_cmd, script] + # Capture submission command return value so that we can # intercept and report basic submission failures; #167 try: - subprocess.check_call(submission_command, shell=True, executable="/bin/bash") + # subprocess.check_call(submission_command, shell=True, executable="/bin/bash") # old way + subprocess.check_call(sub_cmd_list, shell=False) except subprocess.CalledProcessError: fails = ( "" if self.collate else [s.sample_name for s in self._samples]