build.sh

#!/bin/bash

set -euf -o pipefail

generator_version=$(git describe --tags --always)
echo "GATK CWL generator: gatk-cwl-generator-${generator_version}"

VERSIONS=( 3.5-0 3.6-0 3.7-0 3.8-0 4.0.0.0 )

tarbase="gatk-cwl-generator-${generator_version}-gatk_cmdline_tools"

tmpdir=$(mktemp -d)
python_bin=$(which python3)
if [ -z "${USE_EXISTING_PYTHON+x}" ]; then
    echo "Using ${python_bin} to generate temporary virtualenv ${tmpdir}/venv"
    set -x
    ${python_bin} -m virtualenv "${tmpdir}/venv" -p python3
    set +x
    echo "Activating virtualenv in ${tmpdir}/venv"
    set +u # virtualenv activate script references unset vars
    . "${tmpdir}/venv/bin/activate"
    set -u
    echo "Installing requirements in virtualenv"
    set -x
    pip install -r requirements.txt
    set +x
else
    echo "Using existing python enviroment"
fi

builddir="${tmpdir}/${tarbase}"
mkdir -p "${builddir}"
echo "Building CWL in ${builddir} for GATK versions ${VERSIONS[@]}"

for ver in ${VERSIONS[@]}
do
    echo "Generating CWL for GATK version ${ver}"
    set -x
    PYTHONPATH=. python -m gatkcwlgenerator -v ${ver} -o "${builddir}/${ver}" "$@"
    set +x
done

if [ -z "${USE_EXISTING_PYTHON+x}" ]; then
    echo "Deactivating virtualenv"
    deactivate
fi

echo "Generating zip file"
set -x
( cd "${tmpdir}"; zip -r ${tarbase}.zip ${tarbase} )
set +x
cp "${tmpdir}/${tarbase}.zip" ./

echo "Generating tgz file"
set -x
( cd "${tmpdir}"; tar zcvf ${tarbase}.tgz ${tarbase}/ )
set +x
cp "${tmpdir}/${tarbase}.tgz" ./

echo "Generating .tar.bz2 file"
set -x
( cd "${tmpdir}"; tar jcvf ${tarbase}.tar.bz2 ${tarbase}/ )
set +x
cp "${tmpdir}/${tarbase}.tar.bz2" ./

echo "Removing tmpdir: ${tmpdir}"
rm -rf "${tmpdir}"

echo "Done."