FIX: ignores datalad failures

miykael · miykael · commit 1c9e3c789272 · 2017-09-03T18:22:28.000+02:00
diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@
 # pull request on our GitHub repository:
 #     https://github.com/kaczmarj/neurodocker
 #
-# Timestamp: 2017-09-03 16:21:04
+# Timestamp: 2017-09-03 16:21:50
 
 FROM neurodebian:stretch-non-free
 
@@ -200,7 +200,7 @@ RUN echo 'neuro:neuro' | chpasswd && usermod -aG sudo neuro
 USER neuro
 
 # User-defined instruction
-RUN bash -c "source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad get -r -J8 ds000114/sub-0[12]/ses-test/anat && datalad get -r -J8 ds000114/sub-0[12]/ses-test/func/*fingerfootlips* && datalad get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/anat && datalad get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/ses-test/func/*fingerfootlips* && datalad get -r -J8 ds000114/derivatives/freesurfer/sub-0[12] && datalad get -r -J8 ds000114/derivatives/freesurfer/fsaverage5" 
+RUN bash -c "source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad --on-failure ignore get -r -J8 ds000114/sub-0[12]/ses-test/anat && datalad --on-failure ignore get -r -J8 ds000114/sub-0[12]/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/anat && datalad --on-failure ignore get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J8 ds000114/derivatives/freesurfer/sub-0[12] && datalad --on-failure ignore get -r -J8 ds000114/derivatives/freesurfer/fsaverage5" 
 
 # User-defined instruction
 RUN curl -sSL https://osf.io/dhzv7/download?version=3 | tar zx -C /data/ds000114/derivatives/fmriprep
@@ -343,7 +343,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "instruction", \
-    \n      "RUN bash -c \"source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad get -r -J8 ds000114/sub-0[12]/ses-test/anat && datalad get -r -J8 ds000114/sub-0[12]/ses-test/func/*fingerfootlips* && datalad get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/anat && datalad get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/ses-test/func/*fingerfootlips* && datalad get -r -J8 ds000114/derivatives/freesurfer/sub-0[12] && datalad get -r -J8 ds000114/derivatives/freesurfer/fsaverage5\" " \
+    \n      "RUN bash -c \"source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad --on-failure ignore get -r -J8 ds000114/sub-0[12]/ses-test/anat && datalad --on-failure ignore get -r -J8 ds000114/sub-0[12]/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/anat && datalad --on-failure ignore get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J8 ds000114/derivatives/freesurfer/sub-0[12] && datalad --on-failure ignore get -r -J8 ds000114/derivatives/freesurfer/fsaverage5\" " \
     \n    ], \
     \n    [ \
     \n      "instruction", \
@@ -370,7 +370,7 @@ RUN echo '{ \
     \n      "RUN bash -c \"echo c.NotebookApp.ip = \\'0.0.0.0\\' > ~/.jupyter/jupyter_notebook_config.py\" " \
     \n    ] \
     \n  ], \
-    \n  "generation_timestamp": "2017-09-03 16:21:04", \
+    \n  "generation_timestamp": "2017-09-03 16:21:50", \
     \n  "neurodocker_version": "0.2.0-30-g4b9bd64" \
     \n}' > /neurodocker/neurodocker_specs.json
 
diff --git a/create_dockerfile.sh b/create_dockerfile.sh
@@ -26,7 +26,7 @@ docker run --rm kaczmarj/neurodocker generate -b neurodebian:stretch-non-free -p
     --instruction "RUN mkdir /data && chown neuro /data && chmod 777 /data && mkdir /output && chown neuro /output && chmod 777 /output && mkdir /repos && chown neuro /repos && chmod 777 /repos" \
     --instruction "RUN echo 'neuro:neuro' | chpasswd && usermod -aG sudo neuro" \
     --user=neuro \
-    --instruction "RUN bash -c \"source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad get -r -J8 ds000114/sub-0[12]/ses-test/anat && datalad get -r -J8 ds000114/sub-0[12]/ses-test/func/*fingerfootlips* && datalad get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/anat && datalad get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/ses-test/func/*fingerfootlips* && datalad get -r -J8 ds000114/derivatives/freesurfer/sub-0[12] && datalad get -r -J8 ds000114/derivatives/freesurfer/fsaverage5\" " \
+    --instruction "RUN bash -c \"source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad --on-failure ignore get -r -J8 ds000114/sub-0[12]/ses-test/anat && datalad --on-failure ignore get -r -J8 ds000114/sub-0[12]/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/anat && datalad --on-failure ignore get -r -J8 ds000114/derivatives/fmriprep/sub-0[12]/ses-test/func/*fingerfootlips* && datalad --on-failure ignore get -r -J8 ds000114/derivatives/freesurfer/sub-0[12] && datalad --on-failure ignore get -r -J8 ds000114/derivatives/freesurfer/fsaverage5\" " \
     --instruction "RUN curl -sSL https://osf.io/dhzv7/download?version=3 | tar zx -C /data/ds000114/derivatives/fmriprep" \
     --workdir /repos \
     --instruction "RUN cd /repos && git clone https://github.com/neuro-data-science/neuroviz.git && git clone https://github.com/neuro-data-science/neuroML.git && git clone https://github.com/ReproNim/reproducible-imaging.git && git clone https://github.com/miykael/nipype_tutorial.git && git clone https://github.com/jmumford/nhwEfficiency.git && git clone https://github.com/jmumford/R-tutorial.git" \
