From 00decc8acc175d0bb90418c2158dd94fc5e28a85 Mon Sep 17 00:00:00 2001
From: Shujun Ou <shujun.ou.1@gmail.com>
Date: Fri, 4 Dec 2020 08:57:30 -0600
Subject: [PATCH] fix sh getopts not found #122

---
 EDTA_raw.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EDTA_raw.pl b/EDTA_raw.pl
index 904c277..a22a6b9 100755
--- a/EDTA_raw.pl
+++ b/EDTA_raw.pl
@@ -384,7 +384,7 @@
 	print STDERR "Species: $species\n";
 
 	# run TIR-Learner
-	`sh $TIR_Learner -g $genome -s $species -t $threads -l $maxint`;
+	`bash $TIR_Learner -g $genome -s $species -t $threads -l $maxint`;
 	`perl $rename_tirlearner ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa | perl -nle 's/TIR-Learner_//g; print \$_' > $genome.TIR`;
 
 	# clean raw predictions with flanking alignment