From 55b739471d656779f4f2c23fe498700cabcd8765 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <b.cantarel@gmail.com>
Date: Sun, 2 Aug 2020 06:49:59 -0500
Subject: [PATCH] agfusion db location
---
alignment/starfusion.sh | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index a3a5099..2b26813 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -58,10 +58,11 @@ then
export PYENSEMBL_CACHE_DIR="/project/shared/bicf_workflow_ref/singularity_images"
cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "singularity exec /project/shared/bicf_workflow_ref/singularity_images/agfusion.simg agfusion annotate -db /project/shared/bicf_workflow_ref/singularity_images/pyensembl/GRCh38/ensembl92/agfusion.homo_sapiens.92.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
else
+ export PYENSEMBL_CACHE_DIR=/opt
refgeno=${index_path}/CTAT_resource_lib
STAR-Fusion --genome_lib_dir ${refgeno} --min_sum_frags 3 --CPU $NPROC --left_fq ${fq1} --right_fq ${fq2} --examine_coding_effect --output_dir ${pair_id}_star_fusion
cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.tsv ${pair_id}.starfusion.txt
- cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate -db agfusion.homo_sapiens.95.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
+ cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "agfusion annotate -db /usr/local/src/agfusion.homo_sapiens.95.db -g5", $1,"-j5",$4,"-g3",$6,"-j3",$9,"-o",$1"_"$4"_"$6"_"$9}' |grep -v 'LeftGene' |sh
fi
if [[ $filter == 1 ]]
--
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