NighresSingularity.def

# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.9.1
# Timestamp: 2022/10/18 10:00:01 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-slim

%files
build.sh /nighres/
cbstools-lib-files.sh /nighres/
setup.py /nighres/
setup.cfg /nighres/
MANIFEST.in /nighres/
README.rst /nighres/
LICENSE /nighres/
imcntk-lib-files.sh /nighres/
dependencies_sha.sh /nighres/
nighres /nighres/nighres/
docker/jupyter_notebook_config.py /etc/jupyter/

%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

apt-get update -qq
apt-get install -y -q --no-install-recommends \
    openjdk-8-jdk git wget build-essential software-properties-common libffi-dev
apt-get clean
rm -rf /var/lib/apt/lists/*

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 create -y -q --name nighres
conda install -y -q --name nighres \
    "python=3.9" \
    "pip" \
    "jcc" \
    "Nilearn"
sync && conda clean -y --all && sync
sed -i '$isource activate nighres' $ND_ENTRYPOINT


ln -svT "/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)" /docker-java-home

cd /nighres

conda init && . /root/.bashrc && conda activate nighres && conda info --envs && ./build.sh && rm -rf cbstools-public imcn-imaging nighresjava/build nighresjava/src

conda install -y -q --name nighres \
    "jupyterlab"
sync && conda clean -y --all && sync
bash -c "source activate nighres
  pip install --no-cache-dir  \
      ".""
rm -rf ~/.cache/pip/*
sync


test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
su - neuro

cd /home/neuro

echo '{
\n  "pkg_manager": "apt",
\n  "instructions": [
\n    [
\n      "base",
\n      "debian:stretch-slim"
\n    ],
\n    [
\n      "user",
\n      "root"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "install",
\n      [
\n        "openjdk-8-jdk git wget build-essential software-properties-common libffi-dev"
\n      ]
\n    ],
\n    [
\n      "miniconda",
\n      {
\n        "create_env": "nighres",
\n        "conda_install": [
\n          "python=3.9",
\n          "pip",
\n          "jcc",
\n          "Nilearn"
\n        ],
\n        "activate": true
\n      }
\n    ],
\n    [
\n      "env",
\n      {
\n        "JAVA_HOME": "/docker-java-home"
\n      }
\n    ],
\n    [
\n      "env",
\n      {
\n        "JCC_JDK": "/docker-java-home"
\n      }
\n    ],
\n    [
\n      "run",
\n      "ln -svT \"/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)\" /docker-java-home"
\n    ],
\n    [
\n      "copy",
\n      [
\n        "build.sh",
\n        "cbstools-lib-files.sh",
\n        "imcntk-lib-files.sh",
\n        "dependencies_sha.sh",
\n        "setup.py",
\n        "setup.cfg",
\n        "MANIFEST.in",
\n        "README.rst",
\n        "LICENSE",
\n        "/nighres/"
\n      ]
\n    ],
\n    [
\n      "copy",
\n      [
\n        "nighres",
\n        "/nighres/nighres"
\n      ]
\n    ],
\n    [
\n      "workdir",
\n      "/nighres"
\n    ],
\n    [
\n      "run",
\n      "conda init && . /root/.bashrc && conda activate nighres && conda info --envs && ./build.sh && rm -rf cbstools-public imcn-imaging nighresjava/build nighresjava/src"
\n    ],
\n    [
\n      "miniconda",
\n      {
\n        "use_env": "nighres",
\n        "conda_install": [
\n          "jupyterlab"
\n        ],
\n        "pip_install": [
\n          "."
\n        ]
\n      }
\n    ],
\n    [
\n      "copy",
\n      [
\n        "docker/jupyter_notebook_config.py",
\n        "/etc/jupyter",
\n        ""
\n      ]
\n    ],
\n    [
\n      "user",
\n      "neuro"
\n    ],
\n    [
\n      "workdir",
\n      "/home/neuro"
\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 CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"
export JAVA_HOME="/docker-java-home"
export JCC_JDK="/docker-java-home"

%files
build.sh cbstools-lib-files.sh
nighres /nighres/nighres
docker/jupyter_notebook_config.py /etc/jupyter

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