From 420c37861a9265e20ea8df1b53172cae82513d36 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 5 Sep 2020 07:43:02 -0500
Subject: [PATCH] move all export PATH under -z isdocker
---
alignment/starfusion.sh | 4 ----
genect_rnaseq/geneabundance.sh | 2 +-
variants/checkmate.sh | 2 +-
variants/msisensor.sh | 6 ++++--
variants/somatic_vc.sh | 2 +-
variants/svcalling.sh | 2 +-
variants/uni_norm_annot.sh | 2 +-
7 files changed, 9 insertions(+), 11 deletions(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 9bc7050..e60b0b8 100755
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -43,10 +43,6 @@ if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
-fi
-
-if [[ -n $method ]] && [[ $method == 'trinity' ]]
-then
module load trinity/1.6.0
tmphome="/tmp/$USER"
if [[ -z $tmphome ]]
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index bbaf11f..b8e8fdb 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -44,9 +44,9 @@ if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load subread/1.6.1
+ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
fi
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 ${sbam}
diff --git a/variants/checkmate.sh b/variants/checkmate.sh
index 855b168..ddd70c2 100755
--- a/variants/checkmate.sh
+++ b/variants/checkmate.sh
@@ -33,9 +33,9 @@ then
source /etc/profile.d/modules.sh
module load samtools/gcc/1.8 bcftools/gcc/1.8
ncm=/project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py
+ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:/usr/local/bin/:$PATH
if [[ -f /usr/local/bin/ncm.py ]]
then
ncm=/usr/local/bin/ncm.py
diff --git a/variants/msisensor.sh b/variants/msisensor.sh
index 1d27dc8..c2e5916 100755
--- a/variants/msisensor.sh
+++ b/variants/msisensor.sh
@@ -30,8 +30,10 @@ if [[ -z $sbam ]] || [[ -z $index_path ]]; then
usage
fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
-
+if [[ -z $isdocker ]]
+then
+ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
+fi
bedopt=''
if [[ -n $capture ]]
then
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 9923e35..95deb66 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -38,8 +38,8 @@ if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load htslib/gcc/1.8 samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14
+ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
shift $(($OPTIND -1))
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index b01363f..f422e93 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -62,8 +62,8 @@ if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
+ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
mkdir -p temp
if [[ -z $tid ]]
diff --git a/variants/uni_norm_annot.sh b/variants/uni_norm_annot.sh
index 502fa0e..56b45e6 100755
--- a/variants/uni_norm_annot.sh
+++ b/variants/uni_norm_annot.sh
@@ -41,8 +41,8 @@ if [[ -z $isdocker ]]
then
source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
+ export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
mv ${vcf} ${pair_id}.ori.vcf.gz
--
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