Singularity.0.0.2d

Bootstrap: shub
From: khanlab/heudiconv:0.4.3a

%setup
mkdir -p $SINGULARITY_ROOTFS/opt/tar2bids
cp -Rv . $SINGULARITY_ROOTFS/opt/tar2bids

%post

## Install bids-validator
apt-get update && \
apt-get install -y curl git && \
curl -sL https://deb.nodesource.com/setup_8.x | bash - && \
apt-get remove -y curl && \
apt-get install -y nodejs && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

git clone http://github.com/INCF/bids-validator /opt/bids-validator
cd /opt/bids-validator
TAG=0.26.5
git checkout $TAG
sed -i -E "s/0.0.0/$TAG/" package.json
npm install -g /opt/bids-validator


#install gnu parallel
apt-get update
apt-get install -y parallel


#need the below to avoid warnings when running gnu-parallel
apt-get install -y locales
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
echo "LANG=en_US.UTF-8" > /etc/locale.conf
echo "LC_ALL=en_US.UTF-8" >> /etc/locale.conf
locale-gen en_US.UTF-8


%environment
export LANGUAGE="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export LANG="en_US.UTF-8"

export PYTHONPATH=$PYTHONPATH:/opt/tar2bids/heuristics

%runscript
exec /opt/tar2bids/tar2bids $@