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miykaelmiykael
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ENH: update fsl to 5.0.10
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‎Dockerfile

Lines changed: 36 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
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# pull request on our GitHub repository:
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# https://github.com/kaczmarj/neurodocker
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#
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# Timestamp: 2017-09-03 17:45:24
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# Timestamp: 2017-09-03 18:36:53
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FROM neurodebian:stretch-non-free
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@@ -36,8 +36,7 @@ ENTRYPOINT ["/neurodocker/startup.sh"]
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RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends fsl \
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dcm2niix \
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&& apt-get install -y -q --no-install-recommends dcm2niix \
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convert3d \
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ants \
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graphviz \
@@ -98,6 +97,29 @@ RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin
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&& /opt/afni/rPkgsInstall -pkgs ALL \
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&& rm -rf /tmp/*
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#-----------------------------------------------------------
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# Install FSL v5.0.10
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# FSL is non-free. If you are considering commerical use
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# of this Docker image, please consult the relevant license:
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# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
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#-----------------------------------------------------------
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends dc \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& echo "Downloading FSL ..." \
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&& curl -sSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
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| tar zx -C /opt \
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&& /bin/bash /opt/fsl/etc/fslconf/fslpython_install.sh -q -f /opt/fsl \
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&& sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
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&& sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
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&& sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
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&& sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT
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ENV FSLDIR=/opt/fsl \
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PATH=/opt/fsl/bin:$PATH
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# User-defined instruction
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RUN rm -rf /opt/fsl/bin/FSLeyes /opt/fsl/data/first /opt/fsl/fslpython
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#--------------------------
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# Install FreeSurfer v6.0.0
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#--------------------------
@@ -210,15 +232,6 @@ WORKDIR /repos
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# User-defined instruction
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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
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# User-defined instruction
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ENV FSLDIR="/usr/share/fsl"
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# User-defined instruction
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RUN . ${FSLDIR}/5.0/etc/fslconf/fsl.sh
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# User-defined instruction
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ENV PATH="${FSLDIR}/5.0/bin:${PATH}"
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# User-defined instruction
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ENV PATH="${PATH}:/usr/lib/rstudio-server/bin"
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@@ -246,7 +259,6 @@ RUN echo '{ \
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\n [ \
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\n "install", \
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\n [ \
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\n "fsl", \
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\n "dcm2niix", \
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\n "convert3d", \
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\n "ants", \
@@ -280,6 +292,16 @@ RUN echo '{ \
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\n } \
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\n ], \
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\n [ \
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\n "fsl", \
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\n { \
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\n "version": "5.0.10" \
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\n } \
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\n ], \
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\n [ \
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\n "instruction", \
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\n "RUN rm -rf /opt/fsl/bin/FSLeyes /opt/fsl/data/first /opt/fsl/fslpython" \
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\n ], \
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\n [ \
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\n "freesurfer", \
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\n { \
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\n "version": "6.0.0", \
@@ -368,18 +390,6 @@ RUN echo '{ \
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\n ], \
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\n [ \
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\n "instruction", \
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\n "ENV FSLDIR=\"/usr/share/fsl\"" \
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\n ], \
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\n [ \
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\n "instruction", \
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\n "RUN . ${FSLDIR}/5.0/etc/fslconf/fsl.sh" \
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\n ], \
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\n [ \
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\n "instruction", \
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\n "ENV PATH=\"${FSLDIR}/5.0/bin:${PATH}\"" \
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\n ], \
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\n [ \
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\n "instruction", \
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\n "ENV PATH=\"${PATH}:/usr/lib/rstudio-server/bin\" " \
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\n ], \
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\n [ \
@@ -391,7 +401,7 @@ RUN echo '{ \
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\n "RUN bash -c \"echo c.NotebookApp.ip = \\'0.0.0.0\\' > ~/.jupyter/jupyter_notebook_config.py\" " \
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\n ] \
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\n ], \
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\n "generation_timestamp": "2017-09-03 17:45:24", \
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\n "generation_timestamp": "2017-09-03 18:36:53", \
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\n "neurodocker_version": "0.2.0-30-g4b9bd64" \
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\n}' > /neurodocker/neurodocker_specs.json
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‎create_dockerfile.sh

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,9 +5,11 @@
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docker run --rm kaczmarj/neurodocker generate -b neurodebian:stretch-non-free -p apt \
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--instruction "RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -" \
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--install fsl dcm2niix convert3d ants graphviz tree git-annex-standalone vim emacs-nox nano less ncdu tig git-annex-remote-rclone build-essential nodejs r-recommended psmisc libapparmor1 sudo dc \
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--install dcm2niix convert3d ants graphviz tree git-annex-standalone vim emacs-nox nano less ncdu tig git-annex-remote-rclone build-essential nodejs r-recommended psmisc libapparmor1 sudo dc \
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--instruction "RUN apt-get update && apt-get install -yq xvfb mesa-utils libgl1-mesa-dri && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* " \
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--afni version=latest \
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--fsl version=5.0.10 \
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--instruction "RUN rm -rf /opt/fsl/bin/FSLeyes /opt/fsl/data/first /opt/fsl/fslpython" \
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--freesurfer version=6.0.0 min=True \
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--spm version=12 matlab_version=R2017a \
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--instruction "RUN curl -sSL https://dl.dropbox.com/s/lfuppfhuhi1li9t/cifti-data.tgz?dl=0 | tar zx -C / " \
@@ -30,9 +32,6 @@ docker run --rm kaczmarj/neurodocker generate -b neurodebian:stretch-non-free -p
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--instruction "RUN curl -sSL https://osf.io/dhzv7/download?version=3 | tar zx -C /data/ds000114/derivatives/fmriprep" \
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--workdir /repos \
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--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" \
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--instruction "ENV FSLDIR=\"/usr/share/fsl\"" \
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--instruction "RUN . \${FSLDIR}/5.0/etc/fslconf/fsl.sh" \
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--instruction "ENV PATH=\"\${FSLDIR}/5.0/bin:\${PATH}\"" \
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--instruction "ENV PATH=\"\${PATH}:/usr/lib/rstudio-server/bin\" " \
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--instruction "ENV LD_LIBRARY_PATH=\"/usr/lib/R/lib:\${LD_LIBRARY_PATH}\" " \
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--instruction "RUN bash -c \"echo c.NotebookApp.ip = \'0.0.0.0\' > ~/.jupyter/jupyter_notebook_config.py\" " \

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