From 9208a39d3f2f688e40c18df2d6ce25e381926b8e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sun, 10 Apr 2016 22:27:46 -0400
Subject: [PATCH] Fix doctests...
---
.../managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh | 1 -
pulsar/managers/util/job_script/__init__.py | 8 +++++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
index eadad98e..0c533ce0 100644
--- a/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
+++ b/pulsar/managers/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
@@ -1,5 +1,4 @@
#!$shell
-
$integrity_injection
$headers
$slots_statement
diff --git a/pulsar/managers/util/job_script/__init__.py b/pulsar/managers/util/job_script/__init__.py
index 9f144dc5..fffd29fe 100644
--- a/pulsar/managers/util/job_script/__init__.py
+++ b/pulsar/managers/util/job_script/__init__.py
@@ -62,10 +62,12 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
True
>>> 'GALAXY_LIB="None"' in script
True
- >>> script.startswith('#!/bin/sh\\n#PBS -test\\n')
+ >>> script.startswith('#!/bin/bash\\n\\n# The following block can be used by the job system')
+ True
+ >>> 'PBS -test\\n' in script
False
- >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', headers='#PBS -test')
- >>> script.startswith('#!/bin/sh\\n#PBS -test\\n')
+ >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', headers='#PBS -test', integrity_injection='')
+ >>> script.startswith('#!/bin/bash\\n\\n#PBS -test\\n')
True
>>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', slots_statement='GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"')
>>> script.find('GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"\\nexport GALAXY_SLOTS\\n') > 0
--
GitLab