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singularity_recipe
# Generated by Neurodocker version 0.4.1-16-ga36d295
# Timestamp: 2019-02-05 07:14:10 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/kaczmarj/neurodocker
Bootstrap: docker
From: neurodebian:stretch-non-free
%post
export ND_ENTRYPOINT="/neurodocker/startup.sh"
apt-get update -qq
apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
dpkg-reconfigure --frontend=noninteractive locales
update-locale LANG="en_US.UTF-8"
chmod 777 /opt && chmod a+s /opt
mkdir -p /neurodocker
if [ ! -f "$ND_ENTRYPOINT" ]; then
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
echo 'set -e' >> "$ND_ENTRYPOINT"
echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker
apt-get update -qq
apt-get install -y -q --no-install-recommends \
convert3d \
ants \
gcc \
g++ \
graphviz \
tree \
git-annex-standalone \
vim \
emacs-nox \
nano \
less \
ncdu \
tig \
git-annex-remote-rclone \
octave \
netbase \
curl \
gnupg
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
apt-get update -qq
apt-get install -y -q --no-install-recommends \
bc \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libmng1 \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
wget
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
echo "Downloading FSL ..."
mkdir -p /opt/fsl-5.0.11
curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-5.0.11 --strip-components 1
sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT
sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT
sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT
sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT
echo "Installing FSL conda environment ..."
bash /opt/fsl-5.0.11/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.11
apt-get update -qq
apt-get install -y -q --no-install-recommends \
bc \
libxext6 \
libxpm-dev \
libxt6
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
echo "Downloading MATLAB Compiler Runtime ..."
curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin
chmod +x /tmp/MCRInstaller.bin
/tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a"
rm -rf /tmp/*
echo "Downloading standalone SPM ..."
curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip
unzip -q /tmp/spm12.zip -d /tmp
mkdir -p /opt/spm12-r7219
mv /tmp/spm12/* /opt/spm12-r7219/
chmod -R 777 /opt/spm12-r7219
rm -rf /tmp/*
/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit
sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
export PATH="/opt/miniconda-latest/bin:$PATH"
echo "Downloading Miniconda installer ..."
conda_installer="/tmp/miniconda.sh"
curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash "$conda_installer" -b -p /opt/miniconda-latest
rm -f "$conda_installer"
conda update -yq -nbase conda
conda config --system --prepend channels conda-forge
conda config --system --set auto_update_conda false
conda config --system --set show_channel_urls true
sync && conda clean -tipsy && sync
conda create -y -q --name neuro
conda install -y -q --name neuro \
python=3.6 \
pytest \
jupyter \
jupyterlab \
jupyter_contrib_nbextensions \
traits \
pandas \
matplotlib \
scikit-learn \
scikit-image \
seaborn \
nbformat \
nb_conda
sync && conda clean -tipsy && sync
bash -c "source activate neuro
pip install --no-cache-dir \
https://github.com/nipy/nipype/tarball/master \
https://github.com/INCF/pybids/tarball/master \
nilearn \
datalad[full] \
nipy \
nbval \
xlrd"
rm -rf ~/.cache/pip/*
sync
sed -i '$isource activate neuro' $ND_ENTRYPOINT
bash -c 'git clone https://github.com/poldracklab/pydeface.git &&
cd pydeface &&
python setup.py install'
echo '{
\n "pkg_manager": "apt",
\n "instructions": [
\n [
\n "base",
\n "neurodebian:stretch-non-free"
\n ],
\n [
\n "_header",
\n {
\n "version": "generic",
\n "method": "custom"
\n }
\n ],
\n [
\n "install",
\n [
\n "convert3d",
\n "ants",
\n "gcc",
\n "g++",
\n "graphviz",
\n "tree",
\n "git-annex-standalone",
\n "vim",
\n "emacs-nox",
\n "nano",
\n "less",
\n "ncdu",
\n "tig",
\n "git-annex-remote-rclone",
\n "octave",
\n "netbase",
\n "curl",
\n "gnupg"
\n ]
\n ],
\n [
\n "fsl",
\n {
\n "version": "5.0.11"
\n }
\n ],
\n [
\n "spm12",
\n {
\n "version": "r7219",
\n "method": "binaries"
\n }
\n ],
\n [
\n "miniconda",
\n {
\n "conda_install": [
\n "python=3.6",
\n "pytest",
\n "jupyter",
\n "jupyterlab",
\n "jupyter_contrib_nbextensions",
\n "traits",
\n "pandas",
\n "matplotlib",
\n "scikit-learn",
\n "scikit-image",
\n "seaborn",
\n "nbformat",
\n "nb_conda"
\n ],
\n "pip_install": [
\n "https://github.com/nipy/nipype/tarball/master",
\n "https://github.com/INCF/pybids/tarball/master",
\n "nilearn",
\n "datalad[full]",
\n "nipy",
\n "nbval",
\n "xlrd"
\n ],
\n "create_env": "neuro",
\n "activate": true
\n }
\n ],
\n [
\n "run_bash",
\n "git clone https://github.com/poldracklab/pydeface.git &&\\n cd pydeface &&\\n python setup.py install"
\n ],
\n [
\n "env",
\n {
\n "XDG_RUNTIME_DIR": ""
\n }
\n ]
\n ]
\n}' > /neurodocker/neurodocker_specs.json
%environment
export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"
export FSLDIR="/opt/fsl-5.0.11"
export PATH="/opt/fsl-5.0.11/bin:$PATH"
export FORCE_SPMMCR="1"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64"
export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"
export XDG_RUNTIME_DIR=""
%runscript
/neurodocker/startup.sh "$@"
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