Install SAMTools without needing root privileges

installSAMTools.sh

#!/bin/bash

#	This script downloads and installs SAMTools
#	The current version of SAMTools is v1.3

set -e
set -o pipefail

#	What versions of SAMTools are we downloading?
SAMTOOLS_VERSION="1.3"

#	Check for the TAR utility and Wget
if ! `command -v tar > /dev/null 2> /dev/null`; then echo "Failed to find the TAR utility, exiting..."; exit 1; fi
if ! `command -v wget > /dev/null 2> /dev/null`; then echo "Failed to find Wget, exiting..."; exit 1; fi

#	Usage message
function Usage() {
	echo -e "\
`basename $0`:	software_directory
where:			software_directory is the directory to\n\
				download and install SAMTools to \n\
\n\
This script downloads and installs SAMTools: \n\
	The current version of SAMTools is ${SAMTOOLS_VERSION} \n\
\n\
Any previous installations of SAMTools in software_directory will be removed \n\
" >&2
	exit 1
}

#	Export the usage message
export -f Usage

#	Do we have our argument?
if [[ "$#" -ne 1 ]]; then Usage; fi # If not, run Usage
#	Where do we download our files?
SOFT_DIR=$1

#	Change to the software directory
cd "${SOFT_DIR}"
#	Remove any previous SAMTools installation
echo "Removing previous any SAMTools installations..." >&2
rm -rf samtools*
#	Download SAMTools
echo "Downloading SAMTools..." >&2
wget https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2
#	Extract the tarballs
tar -xjf samtools*
#	Change to the SAMTools directory
echo "Installing SAMTools..." >&2
cd samtools*
./configure --prefix=$( pwd ) # Configure, set the install directory to be in this directory
make # Make SAMTools
make install # Install SAMTools
make clean # Clean up excess files
cd bin # Change into the 'bin' directory
echo export PATH=$( pwd ):'$PATH' >> "${HOME}"/.bash_profile # Add a PATH addition for SAMTools to our bash_profile
# Change back to the software directory
cd "${SOFT_DIR}"
#	Clean up the tarballs
echo "Cleaning up leftover files..." >&2
rm samtools*.tar.bz2
#	Final ending message
echo "Run source ~/.bash_profile to finish the installation process" >&2