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bamboo_build.sh
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bamboo_build.sh
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#!/usr/bin/env bash
set -e
################
# DEPENDENCIES #
################
## Load modules
type module >& /dev/null || . /mnt/software/Modules/current/init/bash
module purge
module load git
module load meson
module load ninja
module load boost
module load cram
module load minimap2
module load bedtools
module load samtools
module load datamash
module load gcovr
case "${bamboo_planRepository_branchName}" in
master)
module load pbbam/master
module load pbcopper/master
;;
*)
module load pbbam/develop
module load pbcopper/develop
;;
esac
set -vx
BOOST_ROOT="${BOOST_ROOT%/include}"
# unset these variables to have meson discover all
# boost-dependent variables from BOOST_ROOT alone
unset BOOST_INCLUDEDIR
unset BOOST_LIBRARYDIR
# call the main build+test scripts
export LDFLAGS="-static-libstdc++ -static-libgcc"
source scripts/ci/setup.sh
source scripts/ci/build.sh
source scripts/ci/test.sh
if [[ ${BUILD_NUMBER} == 0 ]]; then
echo "Not installing anything (branch: ${bamboo_planRepository_branchName}), exiting."
exit 0
fi
source scripts/ci/install.sh