Compile SJM with SGE

install_sjm.sh

set -e

INSTALL_DIR=/mnt/xxxxx/sjm/sjm-1.2.0

# ===============
# 1 install tclap
# ===============
echo install tclap ...
wget https://jaist.dl.sourceforge.net/project/tclap/tclap-1.2.2.tar.gz
tar xf tclap-1.2.2.tar.gz
cd tclap-1.2.2
./configure --prefix=$INSTALL_DIR
make -j 8
make install
cd ..

# ===============
# 2 install boost
# ===============
echo install boost ...
sudo yum install boost boost-devel -y

# ===============
# 3 install sjm
# ===============
echo install sjm ...
wget https://github.com/StanfordBioinformatics/SJM/archive/1.2.0.tar.gz
tar xf 1.2.0.tar.gz
cd SJM-1.2.0

./configure \
    --prefix=${INSTALL_DIR} \
	--with-scheduler=SGE \
	--with-pe=mpi \
	CPPFLAGS="-I${INSTALL_DIR}/include"

make -j8
make install

echo install done