Merge pull request #404 from psadil/fix/missing-fs-deps

FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh)

Author: effigies

.circleci/config.yml

@@ -458,6 +458,9 @@ jobs:
           name: Run anatomical workflow on ds005
           no_output_timeout: 2h
           command: |
+            # Remove part of FreeSurfer output to ensure that at least
+            # some of recon-all is attempted
+            rm /tmp/ds005/freesurfer/sub-01/mri/ribbon.mgz
             bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph
       - run:
           name: Combine coverage

Dockerfile

@@ -93,7 +93,7 @@ ENV DEBIAN_FRONTEND="noninteractive" \
     LC_ALL="en_US.UTF-8"
 
 # Some baseline tools
-# bc is needed for FreeSurfer
+# bc, tcsh are needed for FreeSurfer
 # libglu1-mesa is needed for Connectome Workbench
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -105,6 +105,7 @@ RUN apt-get update && \
                     libglu1-mesa \
                     lsb-release \
                     netbase \
+                    tcsh \
                     xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*