Singularity

# Generated by Neurodocker version 0.4.1-9-g1f6df59
# Timestamp: 2018-08-14 18:18:52 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

%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 \
    wget
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


echo "Downloading Convert3D ..."
mkdir -p /opt/convert3d-1.0.0
curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-1.0.0 --strip-components 1

apt-get update -qq
apt-get install -y -q --no-install-recommends \
    ed \
    gsl-bin \
    libglib2.0-0 \
    libglu1-mesa-dev \
    libglw1-mesa \
    libgomp1 \
    libjpeg62 \
    libnlopt-dev \
    libxm4 \
    netpbm \
    r-base \
    r-base-dev \
    tcsh \
    xfonts-base \
    xvfb
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
dpkg -i /tmp/toinstall.deb
rm /tmp/toinstall.deb
curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb
dpkg -i /tmp/toinstall.deb
rm /tmp/toinstall.deb
apt-get install -f
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
gsl2_path="$(find / -name 'libgsl.so.19' || printf '')"
if [ -n "$gsl2_path" ]; then
  ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0";
fi
ldconfig
echo "Downloading AFNI ..."
mkdir -p /opt/afni-latest
curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1
PATH=$PATH:/opt/afni-latest rPkgsInstall -pkgs ALL


echo "Downloading ANTs ..."
mkdir -p /opt/ants-2.2.0
curl -fsSL --retry 5 https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz \
| tar -xz -C /opt/ants-2.2.0 --strip-components 1

echo "Downloading Convert3D ..."
mkdir -p /opt/convert3d-nightly
curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/Nightly/c3d-nightly-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-nightly --strip-components 1

sed -i '$iexport XCPEDIR=/xcpEngine-master' $ND_ENTRYPOINT

sed -i '$iexport FSLDIR=/opt/fsl-5.0.11' $ND_ENTRYPOINT

sed -i '$iexport AFNI_PATH=/opt/afni-latest' $ND_ENTRYPOINT

sed -i '$iexport C3D_PATH=/opt/convert3d-nightly/bin' $ND_ENTRYPOINT

sed -i '$iexport ANTSPATH=/opt/ants-2.2.0' $ND_ENTRYPOINT

sed -i '$iexport PATH=$PATH:$XCPEDIR' $ND_ENTRYPOINT

bash -c 'cd / && wget https://github.com/PennBBL/xcpEngine/archive/master.zip && unzip master.zip'

bash -c 'XCPEDIR=/xcpEngine-master FSLDIR=/opt/fsl-5.0.11 AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin ANTSPATH=/opt/ants-2.2.0 /xcpEngine-master/xcpReset'

bash -c 'export PATH=/opt/afni-latest:$PATH && rPkgsInstall -pkgs ALL && rPkgsInstall -pkgs optparse,pracma,RNifti,svglite,signal,reshape2,ggplot2,lme4'

bash -c ' echo =========================='

bash -c 'cat $ND_ENTRYPOINT'

bash -c ' echo =========================='

echo '{
\n  "pkg_manager": "apt",
\n  "instructions": [
\n    [
\n      "base",
\n      "neurodebian:stretch"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "install",
\n      [
\n        "wget"
\n      ]
\n    ],
\n    [
\n      "fsl",
\n      {
\n        "version": "5.0.11"
\n      }
\n    ],
\n    [
\n      "convert3d",
\n      {
\n        "version": "1.0.0",
\n        "method": "binaries"
\n      }
\n    ],
\n    [
\n      "afni",
\n      {
\n        "version": "latest",
\n        "install_r": "true",
\n        "install_r_pkgs": "true"
\n      }
\n    ],
\n    [
\n      "ants",
\n      {
\n        "version": "2.2.0"
\n      }
\n    ],
\n    [
\n      "convert3d",
\n      {
\n        "version": "nightly"
\n      }
\n    ],
\n    [
\n      "env",
\n      {
\n        "XCPEDIR": "/xcpEngine-master",
\n        "FSLDIR": "/opt/fsl-5.0.11",
\n        "AFNI_PATH": "/opt/afni-latest",
\n        "C3D_PATH": "/opt/convert3d-nightly/bin"
\n      }
\n    ],
\n    [
\n      "add_to_entrypoint",
\n      "export XCPEDIR=/xcpEngine-master"
\n    ],
\n    [
\n      "add_to_entrypoint",
\n      "export FSLDIR=/opt/fsl-5.0.11"
\n    ],
\n    [
\n      "add_to_entrypoint",
\n      "export AFNI_PATH=/opt/afni-latest"
\n    ],
\n    [
\n      "add_to_entrypoint",
\n      "export C3D_PATH=/opt/convert3d-nightly/bin"
\n    ],
\n    [
\n      "add_to_entrypoint",
\n      "export ANTSPATH=/opt/ants-2.2.0"
\n    ],
\n    [
\n      "add_to_entrypoint",
\n      "export PATH=$PATH:$XCPEDIR"
\n    ],
\n    [
\n      "run_bash",
\n      "cd / && wget https://github.com/PennBBL/xcpEngine/archive/master.zip && unzip master.zip"
\n    ],
\n    [
\n      "run_bash",
\n      "XCPEDIR=/xcpEngine-master FSLDIR=/opt/fsl-5.0.11 AFNI_PATH=/opt/afni-latest C3D_PATH=/opt/convert3d-nightly/bin ANTSPATH=/opt/ants-2.2.0 /xcpEngine-master/xcpReset"
\n    ],
\n    [
\n      "run_bash",
\n      "export PATH=/opt/afni-latest:$PATH && rPkgsInstall -pkgs ALL && rPkgsInstall -pkgs optparse,pracma,RNifti,svglite,signal,reshape2,ggplot2,lme4"
\n    ],
\n    [
\n      "run_bash",
\n      " echo =========================="
\n    ],
\n    [
\n      "run_bash",
\n      "cat $ND_ENTRYPOINT"
\n    ],
\n    [
\n      "run_bash",
\n      " echo =========================="
\n    ],
\n    [
\n      "entrypoint",
\n      "/neurodocker/startup.sh /xcpEngine-master/xcpEngine \"$@\""
\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:$PATH"
export C3DPATH="/opt/convert3d-1.0.0"
export PATH="/opt/convert3d-1.0.0/bin:$PATH"
export PATH="/opt/afni-latest:$PATH"
export AFNI_PLUGINPATH="/opt/afni-latest"
export ANTSPATH="/opt/ants-2.2.0"
export PATH="/opt/ants-2.2.0:$PATH"
export C3DPATH="/opt/convert3d-nightly"
export PATH="/opt/convert3d-nightly/bin:$PATH"
export XCPEDIR="/xcpEngine-master"
export FSLDIR="/opt/fsl-5.0.11"
export AFNI_PATH="/opt/afni-latest"
export C3D_PATH="/opt/convert3d-nightly/bin"

%runscript
/neurodocker/startup.sh /xcpEngine-master/xcpEngine "$@"