diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 9bc7050514e97f7443c57425a51cad3aac6491ef..e60b0b85dbaccf1df77a7a6c2177d082f3798c6a 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 bbaf11f1e923f6d46f218987b7a12696e7b00411..b8e8fdb37bea875b3d87c086f9f172c598222a3b 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 855b168723c48b383dd3e328c72a715a54959171..ddd70c2be2c69f34d99d18a0741d3c0594a38c61 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 1d27dc83ee69e9e9f586c93263c4511817470d6a..c2e59167eb7062a60adf5a1d9026e006a543bfdc 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 9923e359071c4e28521bc4e1b002bd5c7303685d..95deb660d21fbf1f74c83dbf15269eeba2be02b3 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 b01363fa80861ac48be8728d8244b78cbaeeb4b6..f422e9390bbc4f4373b8409e0d7f1d6b220c8633 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 502fa0e6d9dedda6cd8567f37eed9f6c801020f0..56b45e683d5ad3a3359dc4bb1383ddf4c8b2200c 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