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ENH: updates nipype_tutorial docker image
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‎Dockerfile

Lines changed: 75 additions & 71 deletions
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# Generated by Neurodocker v0.3.0-dev0.
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# Generated by Neurodocker v0.2.0-15-g89db2ca.
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
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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: 2017-08-25 12:18:04
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# Timestamp: 2017-09-01 15:15:46
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FROM neurodebian:stretch-non-free
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@@ -34,61 +34,38 @@ ENTRYPOINT ["/neurodocker/startup.sh"]
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# User-defined instruction
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RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends dcm2niix convert3d ants graphviz tree git-annex-standalone vim emacs-nox nano less ncdu tig git-annex-remote-rclone xvfb mesa-utils build-essential nodejs \
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RUN apt-get update -qq \
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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 \
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tree \
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git-annex-standalone \
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vim \
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emacs-nox \
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nano \
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less \
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ncdu \
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tig \
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git-annex-remote-rclone \
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build-essential \
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nodejs \
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r-recommended \
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psmisc \
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libapparmor1 \
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sudo \
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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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#--------------------
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# Install AFNI latest
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#--------------------
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ENV PATH=/opt/afni:$PATH
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa \
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libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb \
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&& libs_path=/usr/lib/x86_64-linux-gnu \
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&& if [ -f $libs_path/libgsl.so.19 ]; then \
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ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
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fi \
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# Install libxp (not in all ubuntu/debian repositories) \
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&& apt-get install -yq --no-install-recommends libxp6 \
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|| /bin/bash -c " \
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curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
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&& dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" \
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# Install libpng12 (not in all ubuntu/debian repositories) \
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&& apt-get install -yq --no-install-recommends libpng12-0 \
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|| /bin/bash -c " \
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curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
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&& dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" \
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# Install R \
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&& apt-get install -yq --no-install-recommends \
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r-base-dev r-cran-rmpi \
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|| /bin/bash -c " \
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curl -o /tmp/install_R.sh -sSL https://gist.githubusercontent.com/kaczmarj/8e3792ae1af70b03788163c44f453b43/raw/0577c62e4771236adf0191c826a25249eb69a130/R_installer_debian_ubuntu.sh \
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&& /bin/bash /tmp/install_R.sh" \
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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 AFNI ..." \
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&& mkdir -p /opt/afni \
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&& curl -sSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
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| tar zx -C /opt/afni --strip-components=1 \
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&& /opt/afni/rPkgsInstall -pkgs ALL \
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&& rm -rf /tmp/*
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# User-defined instruction
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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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#-----------------------------------------------------------
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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 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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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends afni \
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fsl \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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#--------------------------
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# Install FreeSurfer v6.0.0
@@ -128,12 +105,14 @@ ENV MATLABCMD=/opt/mcr/v92/toolbox/matlab \
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FORCE_SPMMCR=1 \
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LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:/opt/mcr/v92/runtime/glnxa64:/opt/mcr/v92/bin/glnxa64:/opt/mcr/v92/sys/os/glnxa64:$LD_LIBRARY_PATH
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RUN apt-get update -qq && apt-get install -yq --no-install-recommends psmisc libapparmor1 sudo \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# User-defined instruction
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RUN bash -c "curl -sSL http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.0.0_1.0.2g-1ubuntu11.2_amd64.deb > libssl1.0.0_1.0.2g-1ubuntu11.2_amd64.deb && dpkg -i libssl1.0.0_1.0.2g-1ubuntu11.2_amd64.deb && rm libssl1.0.0_1.0.2g-1ubuntu11.2_amd64.deb"
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# User-defined instruction
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RUN bash -c "curl -sSL http://download2.rstudio.org/rstudio-server-$(curl https://s3.amazonaws.com/rstudio-server/current.ver)-amd64.deb >> rstudio-server-amd64.deb && dpkg -i rstudio-server-amd64.deb && rm rstudio-server-amd64.deb"
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# User-defined instruction
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RUN bash -c "curl http://download2.rstudio.org/rstudio-server-$(curl https://s3.amazonaws.com/rstudio-server/current.ver)-amd64.deb >> rstudio-server-amd64.deb && dpkg -i rstudio-server-amd64.deb && rm rstudio-server-amd64.deb"
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RUN Rscript -e 'install.packages(c("neuRosim", "ggplot2", "fmri", "dplyr", "tidyr", "Lahman", "data.table", "readr"), repos = "http://cran.case.edu")'
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# User-defined instruction
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RUN curl -sSL https://dl.dropbox.com/s/lfuppfhuhi1li9t/cifti-data.tgz?dl=0 | tar zx -C /
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#-------------------------
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# Create conda environment
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#-------------------------
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RUN conda create -y -q --name neuro python=3.6 \
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jupyter jupyterlab traits pandas matplotlib scikit-learn seaborn swig reprozip reprounzip altair traitsui apptools configobj vtk jupyter_contrib_nbextensions bokeh scikit-image codecov cython joblib nitime \
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RUN conda create -y -q --name neuro3 python=3.6 \
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jupyter jupyterlab traits pandas matplotlib scikit-learn seaborn swig reprozip reprounzip altair traitsui apptools configobj vtk jupyter_contrib_nbextensions bokeh scikit-image codecov nitime cython joblib jupyterhub=0.7.2 \
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&& sync && conda clean -tipsy && sync \
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&& /bin/bash -c "source activate neuro \
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&& /bin/bash -c "source activate neuro3 \
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&& pip install -q --no-cache-dir \
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https://github.com/nipy/nibabel/archive/master.zip https://github.com/nipy/nipype/tarball/master nilearn https://github.com/INCF/pybids/archive/master.zip datalad dipy nipy duecredit pymvpa2 mayavi git+https://github.com/jupyterhub/nbrsessionproxy.git" \
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https://github.com/nipy/nibabel/archive/master.zip https://github.com/nipy/nipype/tarball/master nilearn https://github.com/INCF/pybids/archive/master.zip datalad dipy nipy duecredit pymvpa2 mayavi git+https://github.com/jupyterhub/nbserverproxy.git git+https://github.com/jupyterhub/nbrsessionproxy.git https://github.com/satra/mapalign/archive/master.zip pprocess " \
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&& sync
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ENV PATH=/opt/conda/envs/neuro/bin:$PATH
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ENV PATH=/opt/conda/envs/neuro3/bin:$PATH
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# User-defined instruction
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RUN bash -c "source activate neuro && python -m ipykernel install --user --name neuro --display-name Py3-neuro "
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RUN bash -c "source activate neuro3 && python -m ipykernel install --sys-prefix --name neuro3 --display-name Py3-neuro "
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# User-defined instruction
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RUN bash -c "source activate neuro && pip install --pre --upgrade ipywidgets pythreejs "
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RUN bash -c "source activate neuro3 && pip install --pre --upgrade ipywidgets pythreejs "
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# User-defined instruction
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RUN bash -c "source activate neuro && pip install --upgrade https://github.com/maartenbreddels/ipyvolume/archive/23eb91685dfcf200ee82f89ab6f7294f9214db8c.zip && jupyter nbextension install --py --sys-prefix ipyvolume && jupyter nbextension enable --py --sys-prefix ipyvolume "
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RUN bash -c "source activate neuro3 && pip install --upgrade https://github.com/maartenbreddels/ipyvolume/archive/master.zip && jupyter nbextension install --py --sys-prefix ipyvolume && jupyter nbextension enable --py --sys-prefix ipyvolume "
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# User-defined instruction
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RUN bash -c "source activate neuro && jupyter nbextension enable rubberband/main && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main "
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RUN bash -c "source activate neuro3 && jupyter nbextension enable rubberband/main && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main "
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# User-defined instruction
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RUN bash -c "source activate neuro && jupyter serverextension enable --sys-prefix --py nbrsessionproxy && jupyter nbextension install --sys-prefix --py nbrsessionproxy && jupyter nbextension enable --sys-prefix --py nbrsessionproxy "
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RUN bash -c "source activate neuro3 && jupyter serverextension enable --sys-prefix --py nbserverproxy && jupyter serverextension enable --sys-prefix --py nbrsessionproxy && jupyter nbextension install --sys-prefix --py nbrsessionproxy && jupyter nbextension enable --sys-prefix --py nbrsessionproxy "
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# User-defined instruction
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RUN bash -c " source activate neuro3 && pip install git+https://github.com/data-8/gitautosync && jupyter serverextension enable --py nbgitautosync --sys-prefix "
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#-------------------------
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# Create conda environment
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&& sync && conda clean -tipsy && sync
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# User-defined instruction
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RUN bash -c "source activate afni27 && python -m ipykernel install --user --name afni27 --display-name Py2-afni "
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RUN bash -c "source activate neuro3 && python -m ipykernel install --sys-prefix --name afni27 --display-name Py2-afni "
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USER root
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# User-defined instruction
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RUN bash -c "source activate neuro && python -c 'from nilearn import datasets; haxby_dataset = datasets.fetch_haxby()' "
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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
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# User-defined instruction
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RUN bash -c "echo c.NotebookApp.ip = \'0.0.0.0\' > ~/.jupyter/jupyter_notebook_config.py"
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RUN echo 'neuro:neuro' | chpasswd && usermod -aG sudo neuro
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WORKDIR /opt/tutorial
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USER neuro
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# User-defined instruction
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RUN bash -c "source activate neuro3 && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && datalad get -r -J4 ds000114/sub-0[12]/ses-test/ && datalad get -r ds000114/derivatives/fr*/sub-0[12] && datalad get -r ds000114/derivatives/fm*/sub-0[12]/anat && datalad get -r ds000114/derivatives/fm*/sub-0[12]/ses-test && datalad get -r ds000114/derivatives/f*/fsaverage5 "
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# User-defined instruction
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RUN curl -sSL https://osf.io/dhzv7/download?version=3 | tar zx -C /data/ds000114/derivatives/fmriprep
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WORKDIR /home/neuro
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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 PATH="${PATH}:/usr/lib/rstudio-server/bin"
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# User-defined instruction
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ENV LD_LIBRARY_PATH="/usr/lib/R/lib:${LD_LIBRARY_PATH}"
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# User-defined instruction
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RUN bash -c "echo c.NotebookApp.ip = \'0.0.0.0\' > ~/.jupyter/jupyter_notebook_config.py"
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