This script downloads and installs many common bioinformatics programs into $HOME/local

install-bio-programs

#! /usr/bin/env bash

export STAR_VERSION=2.5.3a
export SAMTOOLS_VERSION=1.4.1
export BOWTIE2_VERSION=2.3.2
export SEQAN_VERSION=2.2.0
export FLEXBAR_VERSION=3.0.3
export BITSEQ_VERSION=0.7.5

sudo apt-get install libtbb-dev
sudo apt-get install cmake

mkdir -p $HOME/install
mkdir -p $HOME/local/bin

# STAR
cd $HOME/install
wget https://github.com/alexdobin/STAR/archive/$STAR_VERSION.tar.gz
mv $STAR_VERSION.tar.gz STAR-$STAR_VERSION.tar.gz
tar -xvf STAR-$STAR_VERSION.tar.gz
cd STAR-$STAR_VERSION/source
make STAR
ln -s $HOME/install/STAR-$STAR_VERSION/source/STAR $HOME/local/bin

# samtools
cd $HOME/install
wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
tar -xvf samtools-$SAMTOOLS_VERSION.tar.bz2
cd samtools-$SAMTOOLS_VERSION
make
make prefix=$HOME/local install

# bowtie2
cd $HOME/install
wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/$BOWTIE2_VERSION/bowtie2-$BOWTIE2_VERSION-linux-x86_64.zip
unzip bowtie2-$BOWTIE2_VERSION-linux-x86_64.zip
cd bowtie2-$BOWTIE2_VERSION
find `pwd` -type f -maxdepth 1 -executable -exec ln -s {} $HOME/local/bin \;

# seqan and flexbar
cd $HOME/install
wget https://github.com/seqan/seqan/releases/download/seqan-v$SEQAN_VERSION/seqan-library-$SEQAN_VERSION.tar.xz
tar -xvf seqan-library-$SEQAN_VERSION.tar.xz

wget https://github.com/seqan/flexbar/archive/v$FLEXBAR_VERSION.tar.gz
mv v$FLEXBAR_VERSION.tar.gz flexbar-v$FLEXBAR_VERSION.tar.gz
tar -xvf flexbar-v$FLEXBAR_VERSION.tar.gz

ln -s $HOME/install/seqan-library-$SEQAN_VERSION/include flexbar-$FLEXBAR_VERSION
cd flexbar-$FLEXBAR_VERSION
cmake .
make
ln -s $HOME/install/flexbar-$FLEXBAR_VERSION/flexbar $HOME/local/bin

# BitSeq
cd $HOME/install
wget https://github.com/BitSeq/BitSeq/archive/v$BITSEQ_VERSION.tar.gz
mv v$BITSEQ_VERSION.tar.gz BitSeq-$BITSEQ_VERSION.tar.gz
tar -xvf BitSeq-$BITSEQ_VERSION.tar.gz
cd BitSeq-$BITSEQ_VERSION
make
find `pwd`  -maxdepth 1 -type f -executable -exec ln -s {} $HOME/local/bin \;