A script for preparing a reference for running with piper on Uppmax.

prepareReference.sh

#!/bin/bash -l
#SBATCH -A b2010028
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 10:00:00
#SBATCH -J prepare_ref
#SBATCH -o prepare_ref-%j.out
#SBATCH -e prepare_ref-%j.error

# Author: Johan D

INPUT=$1

module load bioinfo-tools
module load bwa/0.6.2 
module load samtools
module load java/sun_jdk1.6.0_45
module load tophat/2.0.4

bwa index $INPUT
bowtie-build $INPUT ${INPUT%.fasta}
samtools faidx $INPUT
java -Xmx5g -jar /bubo/sw/apps/bioinfo/picard/1.69/kalkyl/CreateSequenceDictionary.jar REFERENCE=$INPUT OUTPUT=${INPUT%.fasta}.dict