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# Generated by Neurodocker version 0.4.1-dev
# Timestamp: 2018-07-22 14:48:54 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' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker
apt-get update -qq
apt-get install -y -q --no-install-recommends \
vim \
wget \
strace \
time \
ncdu \
gnupg \
curl \
procps \
datalad \
git-annex-standalone \
python-nipype \
virtualenv \
python-dcmstack \
python-configparser \
python-funcsigs \
python-pytest \
dcmtk \
python-pip \
python-wheel \
python-setuptools \
python-datalad
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
curl -sL https://deb.nodesource.com/setup_6.x | bash -
apt-get update -qq
apt-get install -y -q --no-install-recommends \
nodejs \
npm
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
npm install -g bids-validator@0.26.11
mkdir /afs /inbox
pip install heudiconv
apt-get update -qq
apt-get install -y -q --no-install-recommends \
cmake \
g++ \
gcc \
git \
make \
pigz \
zlib1g-dev
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix
cd /tmp/dcm2niix
git fetch --tags
git checkout v1.0.20180622
mkdir /tmp/dcm2niix/build
cd /tmp/dcm2niix/build
cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20180622 ..
make
make install
rm -rf /tmp/dcm2niix
echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
useradd --no-user-group --create-home --shell /bin/bash reproin
su - reproin
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 "vim",
\n "wget",
\n "strace",
\n "time",
\n "ncdu",
\n "gnupg",
\n "curl",
\n "procps",
\n "datalad",
\n "git-annex-standalone",
\n "python-nipype",
\n "virtualenv",
\n "python-dcmstack",
\n "python-configparser",
\n "python-funcsigs",
\n "python-pytest",
\n "dcmtk",
\n "python-pip",
\n "python-wheel",
\n "python-setuptools",
\n "python-datalad"
\n ]
\n ],
\n [
\n "run",
\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - "
\n ],
\n [
\n "install",
\n [
\n "nodejs",
\n "npm"
\n ]
\n ],
\n [
\n "run",
\n "npm install -g bids-validator@0.26.11"
\n ],
\n [
\n "run",
\n "mkdir /afs /inbox"
\n ],
\n [
\n "run",
\n "pip install heudiconv"
\n ],
\n [
\n "dcm2niix",
\n {
\n "version": "v1.0.20180622",
\n "method": "source"
\n }
\n ],
\n [
\n "run",
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
\n ],
\n [
\n "user",
\n "reproin"
\n ],
\n [
\n "entrypoint",
\n "/neurodocker/heudiconv.sh"
\n ]
\n ]
\n}' > /neurodocker/neurodocker_specs.json
%environment
export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"
export PATH="/opt/dcm2niix-v1.0.20180622/bin:$PATH"
%runscript
/neurodocker/heudiconv.sh