move all export PATH under -z isdocker

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 ]]

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}
 

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

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

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))
 

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 ]]

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