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[Docker] Install minimized version of FS6 #2024

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Merged
merged 4 commits into from
May 17, 2017
Merged

[Docker] Install minimized version of FS6 #2024

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92d8875
[ENH] Revise CircleCI settings
oesteban May 15, 2017
50fa235
[Docker] Install minimized version of FS6
oesteban May 15, 2017
712bd45
updated freesurfer URL and added ANTS as well
satra May 16, 2017
d32be0b
fix: use new link with fsaverage files for mris_expand
satra May 16, 2017
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31 changes: 22 additions & 9 deletions circle.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,22 +27,35 @@ dependencies:
- mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR
- mkdir -p $HOME/docker $HOME/examples $WORKDIR/tests $WORKDIR/logs $WORKDIR/crashfiles ${CIRCLE_TEST_REPORTS}/tests/
- if [[ ! -e "$HOME/bin/codecov" ]]; then mkdir -p $HOME/bin; curl -so $HOME/bin/codecov https://codecov.io/bash && chmod 755 $HOME/bin/codecov; fi
override:
- if [[ -e "$HOME/docker/cache.tar" ]]; then docker load --input $HOME/docker/cache.tar; fi :
- docker load --input $HOME/docker/cache.tar || true :
timeout: 6000
- docker images
- docker pull nipype/base:latest
override:
# Get data
- if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
- if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
- if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
- if [ "$CIRCLE_TAG" != "" ]; then sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py; fi
# - e=1 && for i in {1..5}; do docker build -f docker/base.Dockerfile --rm=false -t nipype/base:latest . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
# timeout: 21600
- e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:latest -t nipype/nipype:py36 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
# Docker
- docker images
- ? |
e=1 && for i in {1..5}; do
docker build --rm=false -f docker/base.Dockerfile -t nipype/base:latest . && e=0 && break || sleep 15;
done && [ "$e" -eq "0" ]
:
timeout: 21600
- ? |
e=1 && for i in {1..5}; do
docker build --rm=false -t nipype/nipype:latest -t nipype/nipype:py36 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15;
done && [ "$e" -eq "0" ]
:
timeout: 6000
- e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:py27 --build-arg PYTHON_VERSION_MAJOR=2 --build-arg PYTHON_VERSION_MINOR=7 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG-py27 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
- ? |
e=1 && for i in {1..5}; do
docker build --rm=false -t nipype/nipype:py27 --build-arg PYTHON_VERSION_MAJOR=2 --build-arg PYTHON_VERSION_MINOR=7 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG-py27 . && e=0 && break || sleep 15;
done && [ "$e" -eq "0" ]
:
timeout: 6000
- docker save -o $HOME/docker/cache.tar nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 :
- docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py36 nipype/nipype:py27 :
timeout: 6000

test:
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2 changes: 1 addition & 1 deletion docker/base.Dockerfile
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Expand Up @@ -44,7 +44,7 @@ RUN apt-get update && \

WORKDIR /opt
# Installing freesurfer -- do it first so that it is cached early
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
RUN curl -sSL https://www.dropbox.com/s/0ldeovrmh26vabq/recon-all-freesurfer6.min.tgz?dl=0 | tar zxv -C /opt \
--exclude='freesurfer/trctrain' \
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I imagine you can safely remove all of the --excludes.

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this section should suffice:

https://github.com/nipy/mindboggle/blob/master/install/Dockerfile.mindboggle.base#L99

--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
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