#!/bin/sh
cd setTGFamSoftLoc;
wget http://tgfam-finder.snu.ac.kr/data/bowtie2-2.3.1-legacy-linux-x86_64.zip;
wget http://tgfam-finder.snu.ac.kr/data/hmmer-3.1b2-linux-intel-x86_64.tar.gz;
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz;
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz.md5;
wget http://tgfam-finder.snu.ac.kr/data/exonerate-2.2.0-x86_64.tar.gz;
wget http://tgfam-finder.snu.ac.kr/data/tophat-2.1.1.Linux_x86_64.tar.gz;
wget http://tgfam-finder.snu.ac.kr/data/cufflinks-2.2.1.Linux_x86_64.tar.gz;
wget http://tgfam-finder.snu.ac.kr/data/scipio-1.4.zip;
wget http://tgfam-finder.snu.ac.kr/data/augustus-3.2.3.tar.gz;
wget http://tgfam-finder.snu.ac.kr/data/blat.tar.gz;
wget http://tgfam-finder.snu.ac.kr/data/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz;

unzip -o bowtie2-2.3.1-legacy-linux-x86_64.zip;
tar zxvf hmmer-3.1b2-linux-intel-x86_64.tar.gz;
md5sum ncbi-blast-2.6.0+-x64-linux.tar.gz.md5;
tar zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz;
tar zxvf exonerate-2.2.0-x86_64.tar.gz;
tar zxvf tophat-2.1.1.Linux_x86_64.tar.gz;
tar zxvf cufflinks-2.2.1.Linux_x86_64.tar.gz;
unzip -o scipio-1.4.zip;
tar zxvf augustus-3.2.3.tar.gz;
tar zxvf blat.tar.gz;
tar zxvf clustalw-2.1-linux-x86_64-libcppstatic.tar.gz;

rm -rf bowtie2-2.3.1-legacy-linux-x86_64.zip;
rm -rf hmmer-3.1b2-linux-intel-x86_64.tar.gz;
rm -rf ncbi-blast-2.6.0+-x64-linux.tar.gz.md5;
rm -rf ncbi-blast-2.6.0+-x64-linux.tar.gz;
rm -rf exonerate-2.2.0-x86_64.tar.gz;
rm -rf tophat-2.1.1.Linux_x86_64.tar.gz;
rm -rf cufflinks-2.2.1.Linux_x86_64.tar.gz;
rm -rf scipio-1.4.zip;
rm -rf augustus-3.2.3.tar.gz;
rm -rf blat.tar.gz;
rm -rf tar zxvf clustalw-2.1-linux-x86_64-libcppstatic.tar.gz;

yum -y update;
yum -y install gcc gcc-c++;
yum -y install zlib-devel;
yum -y install libpng libpng-devel;
yum -y install ncurses ncurses-devel;

## AUGUSTUS ##
make -C setTGFamSoftLoc/augustus-3.2.3/src/;
export AUGUSTUS_CONFIG_PATH=setTGFamSoftLoc/augustus-3.2.3/config/;
chmod 777 setTGFamSoftLoc/augustus-3.2.3/config;
chmod 777 setTGFamSoftLoc/augustus-3.2.3/config/species;

## Hmmer ##
cd setTGFamSoftLoc/hmmer-3.1b2-linux-intel-x86_64;
setTGFamSoftLoc/hmmer-3.1b2-linux-intel-x86_64/configure;
make -C setTGFamSoftLoc/hmmer-3.1b2-linux-intel-x86_64/;
make check -C setTGFamSoftLoc/hmmer-3.1b2-linux-intel-x86_64/;

## tophat bowtie link ##
cd setTGFamSoftLoc/tophat-2.1.1.Linux_x86_64;

ln -s setTGFamSoftLoc/bowtie2-2.3.1-legacy/bowtie2 setTGFamSoftLoc/tophat-2.1.1.Linux_x86_64/;
