#!/bin/bash

# exit when any command fails
set -e

# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
# echo an error message before exiting
trap 'echo "\"${last_command}\" command filed with exit code $?."' EXIT

[ ! -d "/tmp/install" ] && mkdir /tmp/install
cd /tmp/install
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6/sratoolkit.2.9.6-ubuntu64.tar.gz
gunzip sratoolkit.2.9.6-ubuntu64.tar.gz
tar -xvf sratoolkit.2.9.6-ubuntu64.tar
cp sratoolkit.2.9.6-ubuntu64/bin/fastq-dump /usr/local/bin/
cp sratoolkit.2.9.6-ubuntu64/bin/prefetch /usr/local/bin/
wget https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2
bzip2 -d tabix-0.2.6.tar.bz2
tar -xvf tabix-0.2.6.tar
cd /tmp/install/tabix-0.2.6
make
cp /tmp/install/tabix-0.2.6/bgzip /tmp/install/tabix-0.2.6/tabix /usr/local/bin/
cd /tmp/install
wget https://github.com/bedops/bedops/releases/download/v2.4.39/bedops_linux_x86_64-v2.4.39.tar.bz2
tar jxvf bedops_linux_x86_64-v2.4.39.tar.bz2
cp /tmp/install/bin/* /usr/local/bin/

cd /tmp/install
git clone https://github.com/genome/bam-readcount.git
cd bam-readcount
cmake /tmp/install/bam-readcount
make
cp /tmp/install/bam-readcount/bin/bam-readcount /usr/local/bin/

cd /tmp/install
git clone https://github.com/gpertea/gffcompare
cd gffcompare
make release
cp gffcompare /usr/local/bin/
cp trmap /usr/local/bin

cd /tmp/install
git clone https://github.com/TGAC/KAT.git
cd KAT
./build_boost.sh
./autogen.sh
./configure
make
make install