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#!/bin/bash | |
set -eu | |
# Either to build against to-be-released heudiconv | |
dev_build= | |
generate() { | |
if [ "$dev_build" = "1" ]; then | |
apt_pkgs=python3-pip | |
run_cmd="pip install git+https://github.com/nipy/heudiconv@master" | |
else | |
apt_pkgs="heudiconv=0.9.0-1~nd100+1" | |
run_cmd=":" | |
fi | |
# more details might come on https://github.com/ReproNim/neurodocker/issues/330 | |
[ "$1" == singularity ] && add_entry=' "$@"' || add_entry='' | |
#neurodocker generate "$1" \ | |
ndversion=0.7.0 | |
#ndversion=master | |
docker run --rm repronim/neurodocker:$ndversion generate "$1" \ | |
--base=neurodebian:buster \ | |
--ndfreeze date=20201222T174247Z \ | |
--pkg-manager=apt \ | |
--install vim wget strace time ncdu gnupg curl procps datalad pigz less tree \ | |
git-annex-standalone python3-nibabel \ | |
python3-nipype virtualenv shellcheck \ | |
python3-dcmstack python3-funcsigs python3-etelemetry \ | |
python3-pytest dcmtk python3-pip python3-wheel \ | |
python3-setuptools python3-datalad python3-filelock \ | |
dcm2niix python3-pytest python3-nose $apt_pkgs \ | |
--run "$run_cmd" \ | |
--run "curl -sL https://deb.nodesource.com/setup_9.x | bash - " \ | |
--install nodejs npm \ | |
--run "npm install -g bids-validator@1.5.8" \ | |
--run "mkdir /afs /inbox" \ | |
--user=reproin \ | |
--entrypoint "/usr/bin/heudiconv$add_entry" | |
} | |
version=$(git describe) | |
generate docker > Dockerfile | |
generate singularity > Singularity | |
# Make versioned copy for Singularity Hub | |
cp Singularity Singularity.${version} | |
if [ "$dev_build" != "1" ] && echo $version | grep -e '-g'; then | |
echo "ERROR: Evil Yarik disabled updates of the containers without releases" | |
echo " So this command will 'fail', and if output is alright, reset, tag " | |
echo " (should match frozen version of heudiconv) and redo" | |
exit 1 | |
fi |