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MAINT: create output folder prior to docker run #2106

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Merged
merged 1 commit into from
Apr 28, 2020
Merged

MAINT: create output folder prior to docker run #2106

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6 changes: 5 additions & 1 deletion wrapper/fmriprep_docker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -308,7 +308,8 @@ def __call__(self, parser, namespace, values, option_string=None):
g_dev.add_argument('-e', '--env', action='append', nargs=2, metavar=('ENV_VAR', 'value'),
help='Set custom environment variable within container')
g_dev.add_argument('-u', '--user', action='store',
help='Run container as a given user/uid')
help='Run container as a given user/uid. Additionally, group/gid can be'
'assigned, (i.e., --user <UID>:<GID>)')
g_dev.add_argument('--network', action='store',
help='Run container with a different network driver '
'("none" to simulate no internet connection)')
Expand Down Expand Up @@ -407,6 +408,9 @@ def main():
command.extend(['-v', ':'.join((opts.bids_dir, '/data', 'ro'))])
main_args.append('/data')
if opts.output_dir:
if not os.path.exists(opts.output_dir):
# create it before docker does
os.makedirs(opts.output_dir)
command.extend(['-v', ':'.join((opts.output_dir, '/out'))])
main_args.append('/out')
main_args.append(opts.analysis_level)
Expand Down