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lines changed Original file line number Diff line number Diff line change @@ -26,21 +26,21 @@ dependencies:
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- mkdir -p $WORKDIR && sudo setfacl -d -m group:ubuntu:rwx $WORKDIR && sudo setfacl -m group:ubuntu:rwx $WORKDIR
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- mkdir -p $HOME/docker $HOME/examples $WORKDIR/pytest $WORKDIR/logs
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override :
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- - if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; else echo 'No docker image found in cache'; fi :
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+ - if [[ -e $HOME/docker/cache.tar ]]; then docker load --input $HOME/docker/cache.tar; fi :
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timeout : 6000
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+ - docker images
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- docker pull nipype/base:latest
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- if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi
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- 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 "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi
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- if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi
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- - docker images
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- sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" nipype/info.py
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- # - e=1 && for i in {1..5}; do docker build -f docker/Dockerfile_base --rm=false -t nipype/base:latest . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
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+ # - 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 && [ "$e" -eq "0" ] :
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# timeout: 21600
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- e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:latest -t nipype/nipype:py35 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
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timeout : 6000
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- e=1 && for i in {1..5}; do docker build --rm=false -t nipype/nipype:py27 --build-arg PYTHON_VERSION_MAJOR=2 --build-arg PYTHON_VERSION_MINOR=7 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION=$CIRCLE_TAG-py27 . && e=0 && break || sleep 15; done && [ "$e" -eq "0" ] :
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timeout : 6000
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- - docker save -o $HOME/docker/cache.tar ubuntu:xenial-20161213 nipype/base:latest nipype/nipype:py35 nipype/nipype:py27 :
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+ - docker save -o $HOME/docker/cache.tar nipype/base:latest nipype/nipype:py35 nipype/nipype:py27 :
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timeout : 6000
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test :
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FROM ubuntu:xenial-20161213
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MAINTAINER The nipype developers https://github.com/nipy/nipype
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- # Pre-cache neurodebian key, set noninteractive
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- COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
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+ # Set noninteractive
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ENV DEBIAN_FRONTEND=noninteractive
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- # Installing curl
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+ # Installing requirements for freesurfer installation
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RUN apt-get update && \
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apt-get install -y --no-install-recommends curl ca-certificates && \
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apt-get clean && \
@@ -80,9 +79,10 @@ ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
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PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
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RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
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- # Prepare environment
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+ # Enable neurodebian
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+ COPY docker/files/neurodebian.gpg /etc/apt/neurodebian.gpg
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RUN curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
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- apt-key add /root/. neurodebian.gpg && \
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+ apt-key add /etc/apt/ neurodebian.gpg && \
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apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true
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# Installing general Debian utilities and Neurodebian packages (FSL, AFNI, git)
@@ -166,5 +166,5 @@ ENV MATLABCMD="/opt/mcr/v85/toolbox/matlab" \
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SPMMCRCMD="/opt/spm12/run_spm12.sh /opt/mcr/v85/ script" \
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FORCE_SPMMCR=1
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- WORKDIR /root
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+ WORKDIR /work
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