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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:
Expand Down
50 changes: 18 additions & 32 deletions docker/base.Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -44,39 +44,25 @@ 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 \
--exclude='freesurfer/trctrain' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
--exclude='freesurfer/subjects/fsaverage4' \
--exclude='freesurfer/subjects/fsaverage5' \
--exclude='freesurfer/subjects/fsaverage6' \
--exclude='freesurfer/subjects/cvs_avg35' \
--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/V1_average' \
--exclude='freesurfer/average/mult-comp-cor' \
--exclude='freesurfer/lib/cuda' \
--exclude='freesurfer/lib/qt'

ENV FSL_DIR=/usr/share/fsl/5.0 \
#-----------------------------------------------------------------------------
# 3. Install FreeSurfer v6.0 (minimized with reprozip):
# https://github.com/freesurfer/freesurfer/issues/70
#-----------------------------------------------------------------------------
RUN curl -sSL https://dl.dropbox.com/s/pbaisn6m5qpi9uu/recon-all-freesurfer6-2.min.tgz?dl=0 | tar zx -C /opt
ENV FS_OVERRIDE=0 \
OS=Linux \
FS_OVERRIDE=0 \
FIX_VERTEX_AREA= \
FSF_OUTPUT_FORMAT=nii.gz \
FIX_VERTEX_AREA=\
FREESURFER_HOME=/opt/freesurfer
ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
FUNCTIONALS_DIR=$FREESURFER_HOME/sessions \
MNI_DIR=$FREESURFER_HOME/mni \
LOCAL_DIR=$FREESURFER_HOME/local \
FSFAST_HOME=$FREESURFER_HOME/fsfast \
MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
MNI_DATAPATH=$FREESURFER_HOME/mni/data \
FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
ENV MNI_DIR=$FREESURFER_HOME/mni \
SUBJECTS_DIR=$FREESURFER_HOME/subjects
ENV PERL5LIB=$MNI_DIR/share/perl5 \
MNI_PERL5LIB=$MNI_DIR/share/perl5 \
MINC_BIN_DIR=$MNI_DIR/bin \
MINC_LIB_DIR=$MNI_DIR/lib \
MNI_DATAPATH=$MNI_DIR/data
ENV PATH=$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
ENV FSL_DIR=/usr/share/fsl/5.0
RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh

# Enable neurodebian
Expand Down Expand Up @@ -122,8 +108,8 @@ ENV FSLDIR=/usr/share/fsl/5.0 \

# Installing and setting up ANTs
RUN mkdir -p /opt/ants && \
curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \
| tar -xjC /opt/ants --strip-components 1
curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz?dl=0" \
| tar -zx -C /opt

ENV ANTSPATH=/opt/ants \
PATH=$ANTSPATH:$PATH
Expand Down