From ba389de59b4b32aaf8eea0294cc98753b9cd72d2 Mon Sep 17 00:00:00 2001
From: Arun Seetharam <arnstrm@iastate.edu>
Date: Sun, 8 Oct 2017 11:06:40 -0500
Subject: [PATCH] redundans pipeline, easy and fastway to run!

---
 runRedundans.sh | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 runRedundans.sh

diff --git a/runRedundans.sh b/runRedundans.sh
new file mode 100644
index 0000000..a6a80f3
--- /dev/null
+++ b/runRedundans.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+if [ $# -lt 2 ] ; then
+        echo ""
+        echo "usage: ./runRedundans.sh genome.fasta *.fastq.gz"
+        echo "runs the redundans pipeline using the genome and all fastq files used for the genome assembly"
+        echo "Note: you can softlink all reads (MP and PE) in the directory and supply them as *.fastq.gz for redundans"
+        echo "needs reconfiguration if running using the long reads (pacbio or nanopore)"
+        echo ""
+        exit 0
+fi
+
+module load GIF/redundans
+genome="$1"
+shift
+fastq="$@"
+out="${genome%.*}_redundans_output"
+mkdir -p ${out}
+
+redundans.py \
+     -v \
+     -i ${fastq} \
+     -f ${genome} \
+     -o ${out} \
+     -t 16 \
+     --log redundans_out.log