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galaxy.jobs.runners.util.job_script package

galaxy.jobs.runners.util.job_script.check_script_integrity(config)

galaxy.jobs.runners.util.job_script.job_script(template=<string.Template object>, **kwds)

>>> has_exception = False
>>> try: job_script()
... except Exception as e: has_exception = True
>>> has_exception
True
>>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec')
>>> '\nuptime\n' in script
True
>>> 'echo $? > ec' in script
True
>>> 'GALAXY_LIB="None"' in script
True
>>> script.startswith('#!/bin/sh\n#PBS -test\n')
False
>>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', headers='#PBS -test')
>>> script.startswith('#!/bin/bash\n\n#PBS -test\n')
True
>>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', slots_statement='GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"')
>>> script.find('GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"\n') > 0
True
>>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec', memory_statement='GALAXY_MEMORY_MB="32768"')
>>> script.find('GALAXY_MEMORY_MB="32768"\n') > 0
True

galaxy.jobs.runners.util.job_script.write_script(path, contents, config, mode=493)