From b7202191237bca8c0d4c70ad250eb8b0ebe64da4 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 21 Jul 2020 19:33:23 -0500
Subject: [PATCH] add baseDir to genect_rnaseq/geneabundance.sh
---
genect_rnaseq/geneabundance.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index 35c1d00..7eb6d3f 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -41,7 +41,7 @@ then
fi
source /etc/profile.d/modules.sh
module load subread/1.6.1
-
+baseDir="`dirname \"$0\"`"
export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
featureCounts -s $stranded -M --fraction -J --ignoreDup -T $NPROC -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
--
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