singularity_recipe

gistfile1.txt

# 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 "$@"