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Merge pull request #2203 from jmchilton/doctest_fix

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[16.04] Sync job_script module with Pulsar to fix doctest.
This commit is contained in:
Martin Cech
2016-04-20 11:01:28 -04:00
parent e5290e1964 a9280649b2
commit adbc66873a
1 changed files with 2 additions and 2 deletions
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lib/galaxy/jobs/runners/util/job_script/__init__.py
+2 -2
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@@ -65,7 +65,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
>>> script.startswith('#!/bin/sh\\n#PBS -test\\n')
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.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
@@ -76,7 +76,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
job_instrumenter = kwds.get("job_instrumenter", None)
if job_instrumenter:
del kwds["job_instrumenter"]
working_directory = kwds["working_directory"]
working_directory = kwds.get("metadata_directory", kwds["working_directory"])
kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(working_directory) or ''
kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(working_directory) or ''