Install Platypus on MSI

InstallPlatypusMSI.sh

#!/bin/bash

#   This script is designed to install Platypus on MSI

set -e
set -o pipefail

INSTALL_DIR=${1:-$(pwd)}

echo "Installing Platypus into ${INSTALL_DIR}..." >&2

#   Install HTSLib
echo "Dependency: HTSLib" >&2
wget https://github.com/samtools/htslib/releases/download/1.2.1/htslib-1.2.1.tar.bz2
tar -xvjf htslib-1.2.1.tar.bz2
cd htslib-1.2.1
bash configure --prefix=$(pwd)
make
make install
export C_INClUDE_PATH=$(pwd)/include
export LIBRARY_PATH=$(pwd)/lib
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$(pwd)/lib
cd ..
#   Install Cython
echo "Dependency: Cython" >&2
module load python
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/soft/python/2.7.1/lib
wget http://cython.org/release/Cython-0.23.4.tar.gz
tar -xvzf Cython-0.23.4.tar.gz
cd Cython-0.23.4
export PATH=${PATH}:$(pwd)/bin
export PYTHONPATH=$PYTHONPATH:`pwd`
export PYTHONPATH=$PYTHONPATH:`pwd`/lib/python2.7/site-packages/
python setup.py install --prefix=`pwd`
cd ..
#   Install Platypus
git clone https://github.com/andyrimmer/Platypus.git
cd Platypus
make