#!/bin/sh
# Grid Engine options (lines prefixed with #$)
#$ -N STAR_genome_index # job name
#$ -cwd
#$ -l h_rt=50:00:00
#$ -l h_vmem=16G
#$ -pe sharedmem 6 
#$ -M s1241040@ed.ac.uk   
#$ -m beas 

# Initialise the environment modules
. /etc/profile.d/modules.sh

cd /exports/eddie/scratch/s1241040

module load igmm/apps/STAR/2.7.8a

STAR --runThreadN 6 \
--runMode genomeGenerate \
--genomeDir STAR_Index_Combined \
--genomeFastaFiles Reference_Genomes/refdata-gex-GRCh38-and-mm10-2020-A/fasta/genome.fa \
--sjdbGTFfile Reference_Genomes/refdata-gex-GRCh38-and-mm10-2020-A/genes/genes.gtf \
--genomeSAsparseD 3   



echo "I ran :)"