From f65dccb0ac0c0ae140bfd65a4ad3b4cc3463152a Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 22 Sep 2020 09:02:20 -0500
Subject: [PATCH] correct isdocker norm_annot.sh used by pindel
---
variants/norm_annot.sh | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/variants/norm_annot.sh b/variants/norm_annot.sh
index 445ceab..d282231 100755
--- a/variants/norm_annot.sh
+++ b/variants/norm_annot.sh
@@ -25,9 +25,11 @@ shift $(($OPTIND -1))
baseDir="`dirname \"$0\"`"
if [[ -z $isdocker ]]
- source /etc/profile.d/modules.sh
- module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
+then
+ source /etc/profile.d/modules.sh
+ module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
fi
+
if [[ -a "${index_path}/genome.fa" ]]
then
reffa="${index_path}/genome.fa"
--
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