Created branch and added the automated reference generator process to the programs

generate_reference.sh

+#!/bin/bash
+
+#SBATCH --job-name=PrepareGenome
+#SBATCH --partition=super
+#SBATCH --output=build_chromesizes.%j.out
+#SBATCH --error=build_chromesizes.%j.err
+#SBATCH --mail-user=${USER}@utsouthwestern.edu
+#SBATCH --mail-type=ALL
+
+#Program to create the genomes for use in our standard pipelines.  Assumes that you have already downloaded the GTF and dna.toplevel.fa files
+
+#Setup universal variables
+DIRECTORY=`pwd -P`;
+THREADS=`nproc --all`;
+
+#Create the required genome and gencode files
+zcat *.dna.toplevel.fa.gz > genome.fa &
+zcat *.gtf.gz > gencode.gtf &
+wait;
+
+#Load and run BWA to build index
+module load BWA/0.7.5;
+bwa index -a bwtsw genome.fa;
+module rm BWA/0.7.5;
+
+#Run Hisat 2
+module load hisat2/2.1.0-intel;
+mkdir hisat_index;
+hisat2-build -p ${THREADS} genome.fa hisat_index/genome;
+module rm hisat2/2.1.0-intel;
+
+#Run Star
+module load star;
+mkdir star_index;
+STAR --runMode genomeGenerate --genomeDir star_index --genomeFastaFiles genome.fa --sjdbGTFfile gencode.gtf --runThreadN ${THREADS};
+rm -rf _STARtmp;
+module rm star/2.5.2b;
+
+#Get genoome sizes
+module load samtools/gcc/1.6;
+samtools faidx genome.fa && cut -f1,2 genome.fa.fai > sizes.genome && module rm samtools/gcc/1.6 &
+
+#Wait and build Bowtie2 Index
+wait;
+module load bowtie2/2.2.8-intel;
+bowtie2-build -f genome.fa genome;
+
+#Exit
+exit 0;