From bbb0cfbd7c46a26ba1869e15db7b5c816ae9c867 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 28 Apr 2020 10:22:49 -0400 Subject: [PATCH] MAINT: create output folder prior to docker run --- wrapper/fmriprep_docker.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/wrapper/fmriprep_docker.py b/wrapper/fmriprep_docker.py index 2261582cd..a15214d53 100755 --- a/wrapper/fmriprep_docker.py +++ b/wrapper/fmriprep_docker.py @@ -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 :)') g_dev.add_argument('--network', action='store', help='Run container with a different network driver ' '("none" to simulate no internet connection)') @@ -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)