[skip docs][skip ds054][skip ds210][skip tests] update fmriprep-docker

Author: oesteban

.circleci/config.yml

@@ -201,7 +201,7 @@ jobs:
           name: Run fMRIPrep tests
           no_output_timeout: 2h
           command: |
-            docker run -u 1000 -ti --rm=false \
+            docker run -ti --rm=false \
               --entrypoint="py.test" poldracklab/fmriprep:latest \
               /root/src/fmriprep/ --doctest-modules --ignore=docs --ignore=setup.py
       - run:
@@ -264,7 +264,7 @@ jobs:
           name: Build fMRIPrep documentation
           no_output_timeout: 2h
           command: |
-            docker run -u 1000 -ti --rm=false -v $PWD:/_build_html \
+            docker run -ti --rm=false -v $PWD:/_build_html \
               --entrypoint=sphinx-build poldracklab/fmriprep:latest \
               -T -E -b html -d _build/doctrees-readthedocs -W -D \
               language=en /root/src/fmriprep/docs/ /_build_html 2>&1 \
@@ -326,7 +326,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --debug --write-graph --mem_mb 4096 \
@@ -346,7 +346,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --debug --write-graph --use-syn-sdc --mem_mb 4096 \
@@ -373,7 +373,7 @@ jobs:
           command: |
             rm /tmp/data/ds005/sub-01/func/*_run-02_*
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
                 --debug --write-graph --use-syn-sdc --mem_mb 4096 \

wrapper/fmriprep_docker.py

@@ -286,6 +286,8 @@ def get_parser():
                        type=os.path.abspath, help='Use custom nipype.cfg file')
     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')
 
     return parser
 
@@ -363,6 +365,9 @@ def main():
         for envvar in opts.env:
             command.extend(['-e', '%s=%s' % tuple(envvar)])
 
+    if opts.user:
+        command.extend(['-e', opts.user])
+
     if opts.fs_license_file:
         command.extend([
             '-v', '{}:/opt/freesurfer/license.txt:ro'.format(