#!/bin/bash

##create path for AASRA in /usr/local
sudo mkdir -p /usr/local/AASRA

##install bowtie2
unzip bowtie2-2.1.0-source.zip
cd bowtie2-2.1.0
sudo make
sudo cp bowtie* /usr/local/AASRA
cd ..

##install featureCounts
tar zxvf subread-1.5.2-source.tar.gz
cd subread-1.5.2-source/src
sudo make -f Makefile.Linux
cd ../bin
sudo cp featureCounts /usr/local/AASRA
cd ../..

##install AASRA
sudo chmod 755 AASRA*
sudo cp AASRA* /usr/local/AASRA

echo
echo "AASRA Installation complete."
echo
echo "Executable files of AASRA and dependencies are located in the directory: /usr/local/AASRA"
echo