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#!/bin/bash
set -e
while getopts "sb:" opt; do
case $opt in
s) use_sra=1 ;;
b) branch="$OPTARG" ;;
*) echo "Usage: $0 [-s] [-b <branch_name>]" && exit 1
esac
done
shift $(($OPTIND - 1))
if [ "$branch" == "" ] ; then
branch="master"
fi
set -x
yum install -y git zip unzip pandoc
git clone --recursive https://github.com/BenLangmead/bowtie2.git
if [ $? -ne 0 ] ; then
echo "Unable to clone bowtie2 repo"
exit 1
fi
cd bowtie2
git branch -a | grep "$branch" 2>&1 > /dev/null
if [ $? -ne 0 ] ; then
echo "branch '$branch' does not exist"
exit 1
else
git checkout "$branch"
fi
if [ $use_sra -eq 1 ] ; then
# this variant is needed to compile ncbi-vdb
source /hbb/activate
yum install -y java-1.8.0-openjdk-devel.$(uname -m)
make sra-deps
fi
# this variant creates static binaries with PIC
source /hbb_exe_gc_hardened/activate
# this version of pandoc does not support 'smart' filters
sed -i 's/-smart//' Makefile
make static-libs
if [ $? -ne 0 ] ; then
echo "Unable to build tbb and/or zlib static dependencies"
exit 1
fi
make bowtie2-bin-pkg STATIC_BUILD=1 WITH_ZSTD=1 USE_SRA=$use_sra
if [ $? -ne 0 ] ; then
echo "Unable to create bowtie2 package"
exit 1
fi
echo "Running libcheck..."
libcheck bowtie2-{align,build,inspect}-*
echo "Running hardening check..."
hardening-check -b bowtie2-{align,build,inspect}-*
echo "Copying binary package"
cp /bowtie2/*.zip /io
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