slurm_red.sh

#!/bin/bash

# @Author: Tobias Jakobi <tjakobi>
# @Date:   Friday, May 6, 2016 4:10 PM
# @Email:  tobias.jakobi@med.uni-heidelberg.de
# @Project: University Hospital Heidelberg, Section of Bioinformatics and Systems Cardiology
# @Last modified by:   tjakobi
# @Last modified time: Friday, May 6, 2016 4:22 PM
# @License: CC BY-NC-SA

#SBATCH -n 1
#SBATCH -N 1
#SBATCH -c2 
#SBATCH --mem=20G
#SBATCH -J "red"
#SBATCH --mail-type=END,FAIL,TIME_LIMIT_80
#SBATCH --mail-user=tobias.jakobi@med.uni-heidelberg.de

#module load star

# check if we have 6 arguments
if [ ! $# == 3 ]; then
  echo "Usage: $0 [STAR index] [Read 1 file] [Read 2 file] [target dir e.g. /tmp/] [Read 1 marker, e.g. R1] [GTF file]"
  exit
fi

# $1 -> Genome index
# $2 -> Read 1
# $3 -> Read 2
# $4 -> Target directory

# remove the file extension and potential "R1" markings
# (works for double extension, e.g. .fastq.gz)

mkdir -pv $3

perl /home/tjakobi/tmp/RED-ML/bin/red_ML.pl --rnabam ${1} --reference ${2} --dbsnp /home/tjakobi/tmp/RED-ML/database/00-All.vcf --outdir $3