From bceadcbcbe589bc2335ca0302a6a4069f0516adb Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 11 Feb 2019 11:45:45 -0600
Subject: [PATCH] update agfusion
---
alignment/filter_genefusions.pl | 2 ++
alignment/starfusion.sh | 2 +-
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/alignment/filter_genefusions.pl b/alignment/filter_genefusions.pl
index 44b4453..f44cf58 100755
--- a/alignment/filter_genefusions.pl
+++ b/alignment/filter_genefusions.pl
@@ -29,6 +29,8 @@ while (my $line = <OM>) {
my @exonfiles = `ls */*.exons.txt`;
foreach $efile (@exonfiles) {
chomp($efile);
+ my @leftexons;
+ my @rightexons;
my ($dir,$pair,@etc) = split(/\/|\./,$efile);
open EFILE, "<$efile" or die $!;
my $header = <EFILE>;
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 73599fb..d462f5a 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -60,7 +60,7 @@ else
cp ${pair_id}_star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt
fi
-module load singularity/2.6.1
+module load singularity/3.0.2
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
--
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