singularity.def

# Generated by: Neurodocker version 0.7.0+12.g913b321
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2020/07/20 21:49:03 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/ReproNim/neurodocker

Bootstrap: docker
From: debian:stretch

%post
su - root

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/*
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' >> "$ND_ENTRYPOINT"
  echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker

echo "Downloading MRtrix3 ..."
mkdir -p /opt/mrtrix3-3.0.0
curl -fsSL --retry 5 https://github.com/kaczmarj/MRtrix3-builds/releases/download/3.0.0/mrtrix3-3.0.0-Linux-centos6-x86_64.tar.gz \
| tar -xz -C /opt/mrtrix3-3.0.0 --strip-components 1

echo "Downloading ANTs ..."
mkdir -p /opt/ants-2.3.1
curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
| tar -xz -C /opt/ants-2.3.1 --strip-components 1

apt-get update -qq
apt-get install -y -q --no-install-recommends \
    bc \
    dc \
    file \
    libfontconfig1 \
    libfreetype6 \
    libgl1-mesa-dev \
    libgl1-mesa-dri \
    libglu1-mesa-dev \
    libgomp1 \
    libice6 \
    libxcursor1 \
    libxft2 \
    libxinerama1 \
    libxrandr2 \
    libxrender1 \
    libxt6 \
    sudo \
    wget
apt-get clean
rm -rf /var/lib/apt/lists/*
echo "Downloading FSL ..."
mkdir -p /opt/fsl-6.0.3
curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.3 --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-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3

apt-get update -qq
apt-get install -y -q --no-install-recommends \
    dirmngr \
    gnupg2
apt-get clean
rm -rf /var/lib/apt/lists/*
curl -fsSL --retry 5 http://neuro.debian.net/lists/stretch.us-nh.full \
> /etc/apt/sources.list.d/neurodebian.sources.list
curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg | apt-key add -
(apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true)
apt-get -qq update


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 -y --all && sync
conda install -y -q --name base \
    "python=3.7.3" \
    "pip=20.0.2" \
    "dipy" \
    "nipype" \
    "nibabel" 
sync && conda clean -y --all && sync
bash -c "source activate base
  pip install --no-cache-dir  \
      "pybids" \
      "fastcore" \
      "nilearn" \
      "pipetography==0.3.12""
rm -rf ~/.cache/pip/*
sync


apt-get update -qq
apt-get install -y -q --no-install-recommends \
    git \
    ssh \
    tar \
    gzip \
    ca-certificates \
    fsl-first-data
apt-get clean
rm -rf /var/lib/apt/lists/*

ldconfig

echo '{
\n  "pkg_manager": "apt",
\n  "instructions": [
\n    [
\n      "base",
\n      "debian:stretch"
\n    ],
\n    [
\n      "user",
\n      "root"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "mrtrix3",
\n      {
\n        "version": "3.0_RC3"
\n      }
\n    ],
\n    [
\n      "ants",
\n      {
\n        "version": "2.3.1"
\n      }
\n    ],
\n    [
\n      "fsl",
\n      {
\n        "version": "6.0.1"
\n      }
\n    ],
\n    [
\n      "miniconda",
\n      {
\n        "use_env": "base",
\n        "conda_install": [
\n          "python=3.7.3",
\n          "pip=20.0.2",
\n          "dipy",
\n          "nipype",
\n          "nibabel"
\n        ],
\n        "pip_install": [
\n          "pybids",
\n          "fastcore",
\n          "nilearn",
\n          "pipetography==0.3.12"
\n        ]
\n      }
\n    ],
\n    [
\n      "install",
\n      [
\n        "git",
\n        "ssh",
\n        "tar",
\n        "gzip",
\n        "ca-certificates"
\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 PATH="/opt/mrtrix3-3.0.0/bin:$PATH"
export ANTSPATH="/opt/ants-2.3.1"
export PATH="/opt/ants-2.3.1:$PATH"
export FSLDIR="/opt/fsl-6.0.3"
export PATH="/opt/fsl-6.0.3/bin:$PATH"
export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLMULTIFILEQUIT="TRUE"
export FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh"
export FSLWISH="/opt/fsl-6.0.3/bin/fslwish"
export FSLLOCKDIR=""
export FSLMACHINELIST=""
export FSLREMOTECALL=""
export FSLGECUDAQ="cuda.q"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/miniconda-latest/lib/"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"

%runscript
/neurodocker/startup.sh "$@"