DavidEWarrenPhD/afnipype:latest

$ singularity pull shub://DavidEWarrenPhD/afnipype:latest

Singularity Recipe

# Generated by Neurodocker version 0.4.3-6-g12a2b6f
# Timestamp: 2019-03-06 02:49:12 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: debian: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 \
    vim \
    python
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

su - root

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 \
    libxm4 \
    netpbm \
    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

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

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_py36
conda install -y -q --name neuro_py36 \
    'python=3.6' \
    'matplotlib' \
    'numpy' \
    'pandas' \
    'scikit-learn' \
    'nilearn' \
    'scipy' \
    'seaborn' \
    'traits'
sync && conda clean -tipsy && sync
bash -c "source activate neuro_py36
  pip install --no-cache-dir  \
      'nibabel' \
      'nipype'"
rm -rf ~/.cache/pip/*
sync
sed -i '$isource activate neuro_py36' $ND_ENTRYPOINT


echo '{
\n  "pkg_manager": "apt",
\n  "instructions": [
\n    [
\n      "base",
\n      "debian:stretch"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "install",
\n      [
\n        "vim",
\n        "python"
\n      ]
\n    ],
\n    [
\n      "user",
\n      "root"
\n    ],
\n    [
\n      "afni",
\n      {
\n        "version": "latest",
\n        "method": "binaries"
\n      }
\n    ],
\n    [
\n      "user",
\n      "neuro"
\n    ],
\n    [
\n      "miniconda",
\n      {
\n        "conda_install": [
\n          "python=3.6",
\n          "matplotlib",
\n          "numpy",
\n          "pandas",
\n          "scikit-learn",
\n          "nilearn",
\n          "scipy",
\n          "seaborn",
\n          "traits"
\n        ],
\n        "pip_install": [
\n          "nibabel",
\n          "nipype"
\n        ],
\n        "create_env": "neuro_py36",
\n        "activate": true
\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/afni-latest:$PATH"
export AFNI_PLUGINPATH="/opt/afni-latest"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"

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

Collection

• Name: DavidEWarrenPhD/afnipype
• License: None

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