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|
#!/bin/bash
set -e
# from http://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash
no_native_arch=false
cxxflags=""
while [[ $# > 1 ]]
do
key="$1"
case $key in
-b|--branch)
branch="$2"
shift # past argument
;;
-v|--version)
version="$2"
shift # past argument
;;
-f|--cxxflags)
cxxflags="$2"
shift # past argument
;;
--no-native)
no_native_arch=true
;;
*)
# unknown option
;;
esac
shift # past argument or value
done
echo "Building rapmap [branch = ${branch}]. Tagging version as ${version}"
if [ "$no_native_arch" = true ] ; then
echo "Disabling -march=native"
fi
if [[ -z $cxxflags ]] ; then
echo "Passed CXXFLAGS ${cxxflags}"
fi
# Activate Holy Build Box environment.
source /hbb_exe/activate
set -x
# Install things we need
yum install -y --quiet wget
wget http://download.fedoraproject.org/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm
rpm -i --quiet epel-release-5-4.noarch.rpm
#yum install -y --quiet git
#yum install -y --quiet xz-devel.x86_64
#yum install -y --quiet bzip2-devel.x86_64
yum install -y --quiet unzip
curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${branch}.zip -o ${branch}.zip
unzip ${branch}.zip
mv RapMap-${branch} RapMap
cd RapMap
mkdir build
cd build
if [ "$no_native_arch" = true ] ; then
cmake -DFETCH_BOOST=TRUE -DCMAKE_CXX_FLAGS=${cxxflags} -DNO_NATIVE_ARCH=TRUE ..
else
cmake -DFETCH_BOOST=TRUE -DCMAKE_CXX_FLAGS=${cxxflags} ..
fi
make
make install
make test
cd ../scripts
bash make-release.sh -v ${version} -n linux_x86-64
cd ../RELEASES
cp *.tar.gz /io/
|
