From 6d29a48f08b160abaf142fedf82ab1b1a8a3d389 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 12 Feb 2020 10:28:44 -0600
Subject: [PATCH] add baseDir to trimGalore

---
 preproc_fastq/trimgalore.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index e1e2966..c9f00d1 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -22,6 +22,7 @@ do
 done
 
 shift $(($OPTIND -1))
+baseDir="`dirname \"$0\"`"
 
 # Check for mandatory options
 if [[ -z $pair_id ]] || [[ -z $fq1 ]]; then
-- 
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