pals_singularity.def

# Most of this definition file was generated automatically using Neurodocker:
#     https://github.com/ReproNim/neurodocker
# Some modifications were made to include PALS.

Bootstrap: docker
From: ubuntu:18.04

%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 \
    git

apt-get install -y -q --no-install-recommends build-essential
apt-get install -y -q --no-install-recommends python3.8 python3.8-dev python3-pip
apt-get install -y -q --no-install-recommends python3-setuptools
apt-get install -y freeglut3 libsdl1.2debian
apt-get install -y libgtk2.0-dev libgtk-3-dev libwebkitgtk-dev libwebkitgtk-3.0-dev
apt-get install -y libjpeg-turbo8-dev libtiff5-dev libsdl1.2-dev libgstreamer1.0-dev libgstreamer-plugins-base1.0-dev libnotify-dev freeglut3-dev

# Get PALS
git clone https://github.com/npnl/PALS /PALS

python3.8 -m pip install --upgrade pip
python3.8 -m pip install -r /PALS/requirements.txt

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

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


echo '{
\n  "pkg_manager": "apt",
\n  "instructions": [
\n    [
\n      "base",
\n      "ubuntu:18.04"
\n    ],
\n    [
\n      "user",
\n      "root"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "fsl",
\n      {
\n        "version": "6.0.3",
\n        "method": "binaries"
\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-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"

%runscript
#!/bin/bash
echo "Some packages in this Singularity container are non-free"
echo "If you are considering commercial use of this container, please consult the relevant license:"
echo "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence"

python3.8 /PALS/pals_workflow.py $@