Singularity

Bootstrap: docker
From: debian:buster
%files
requirements.txt ./
. .
%post

DEBIAN_FRONTEND="noninteractive"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
PATH="/opt/dcm2niix-latest/bin:/bet2/bin:$PATH"
apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip \
cmake \
git \
python-setuptools \
python3 \
python3-dev \
python-dev \
python-pip \
g++ \
gcc \
git \
make \
pigz \
zlib1g-dev \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG="en_US.UTF-8" \
&& git clone https://github.com/liangfu/bet2.git /bet2 \
&& mkdir /bet2/build && cd /bet2/build && cmake .. && make \
&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
&& mkdir /tmp/dcm2niix/build \
&& cd /tmp/dcm2niix/build \
&& cmake  -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-latest .. \
&& make \
&& make install \
&& rm -rf /tmp/dcm2niix
cd /src
pip install -r requirements.txt
python setup.py install
cd /output
%environment
export DEBIAN_FRONTEND="noninteractive"
export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export PATH="/opt/dcm2niix-latest/bin:/bet2/bin:$PATH"
%runscript
cd /output
exec tgv_qsm  "$@"
%startscript
cd /output
exec tgv_qsm  "$@"