#!/bin/bash

#instal·lacio dels programes
export PATH=/cursos/BI/bin:$PATH
export PATH=/cursos/BI/bin/ncbiblast/x64/bin:$PATH
cp /cursos/BI/bin/ncbiblast/.ncbirc ~/
export PATH=/cursos/BI/soft/exonerate/x86_64/bin:$PATH
export PATH=/cursos/BI/soft/t_coffee/x86_64/bin:$PATH
export PATH=/cursos/BI/soft/genewise/x86_64/bin:$PATH
export WISECONFIGDIR=/cursos/BI/soft/genewise/x86_64/wise2.2.0/wisecfg/
echo "programes have been successfully installed"

#fastaindex
fastaindex /cursos/BI/genomes/2015/Periophthalmodon_schlosseri/genome.fa PS.index
echo "PS.index has been created"

#Index llargada contigs
fastalength /cursos/BI/genomes/2015/Periophthalmodon_schlosseri/genome.fa > llargada_cromosomes
echo "contig length index has been created"


#Cridem el programa prova.pl
chmod u+x prova.pl
./prova.pl

