From 1f6c3efe48468fa1ab106f2be3af7adf8b3e4b76 Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 1 Feb 2019 11:10:20 -0600
Subject: [PATCH] Created branch and added the automated reference generator
 process to the programs

---
 generate_reference.sh | 49 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 generate_reference.sh

diff --git a/generate_reference.sh b/generate_reference.sh
new file mode 100644
index 0000000..bf00d96
--- /dev/null
+++ b/generate_reference.sh
@@ -0,0 +1,49 @@
+#!/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;
-- 
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