diff --git a/alignment/bam2tdf.sh b/alignment/bam2tdf.sh
index e6299d58137337fa2ded981c5239809c2ecf8e43..1834c773216b5d39c48dbe346a7f1ba16eaa51ac 100755
--- a/alignment/bam2tdf.sh
+++ b/alignment/bam2tdf.sh
@@ -30,8 +30,10 @@ then
 fi
 
 baseDir="`dirname \"$0\"`"
-
-source /etc/profile.d/modules.sh
-module load igvtools/2.3.71 samtools/1.6
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load igvtools/2.3.71 samtools/1.6
+exit
 samtools index  -@ $NPROC $bam
 igvtools count -z 5 $bam ${pair_id}.tdf ${index_path}/igv/human.genome
diff --git a/alignment/hisat_genotype.sh b/alignment/hisat_genotype.sh
index 4ee37c672dea6910e9f0a8e9b8516e55ed4d35b6..97e3f719ceb3f9cdfcec8461225220fd7a91a0eb 100755
--- a/alignment/hisat_genotype.sh
+++ b/alignment/hisat_genotype.sh
@@ -35,9 +35,11 @@ then
     NPROC=`nproc`
 fi
 
-source /etc/profile.d/modules.sh
-module load hisat-genotype/1.0.1
-
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load hisat-genotype/1.0.1
+fi
 diff $fq1 $fq2 > difffile
 
 if [ -s difffile ]
diff --git a/alignment/indexbams.sh b/alignment/indexbams.sh
index 2af125dd027eac1ad1ae2cefd1f776e0a9bc17a5..ecdab135ba10b8bbe7e2b9dee4e4db59577f421d 100755
--- a/alignment/indexbams.sh
+++ b/alignment/indexbams.sh
@@ -26,8 +26,12 @@ fi
 
 baseDir="`dirname \"$0\"`"
 
-source /etc/profile.d/modules.sh
-module load samtools/1.6
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load samtools/1.6
+fi
+
 for i in *.bam; do
     samtools index -@ $NPROC ${i}
 done 
diff --git a/genect_rnaseq/statanal.sh b/genect_rnaseq/statanal.sh
index 23efcf1a0d71687ffbee469dec947b63228cbaeb..cdf3b1cc3bff190c25dc9cd332e9caf2efad399e 100644
--- a/genect_rnaseq/statanal.sh
+++ b/genect_rnaseq/statanal.sh
@@ -25,8 +25,10 @@ if [[ -z $NPROC ]]
 then
     NPROC=`nproc`
 fi
-source /etc/profile.d/modules.sh
-
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+fi
 perl $baseDir/concat_cts.pl -o ./ *.cts
 perl $baseDir/concat_fpkm.pl -o ./ *.fpkm.txt
 perl $baseDir/concat_ctsum.pl -o ./ *.cts.summary
diff --git a/variants/itdseek.sh b/obsolete/itdseek.sh
similarity index 100%
rename from variants/itdseek.sh
rename to obsolete/itdseek.sh
diff --git a/variants/pindel.sh b/obsolete/pindel.sh
similarity index 100%
rename from variants/pindel.sh
rename to obsolete/pindel.sh
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index a4ff47e47d4e3ec6ef953a04d4f1e41affc8c648..334d7d691a2cb1312d4454f270c1c757b4835284 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -107,6 +107,12 @@ then
     fi
     bamlist=`join_by , *.bam`
     Platypus.py callVariants --minMapQual=0 --minReads=3 --mergeClusteredVariants=1 --nCPU=$NPROC --bamFiles=${bamlist} --refFile=${reffa} --output=platypus.vcf
+    for i in *.bam
+    do
+	prefix="${i%.bam}"
+	sid=`samtools view -H ${i} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+	perl -pi -e "s/$prefix/$sid/g" platypus.vcf
+    done
     vcf-sort platypus.vcf |vcf-annotate -n --fill-type -n |bgzip > platypus.vcf.gz
     tabix platypus.vcf.gz
     bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.platypus.vcf.gz platypus.vcf.gz
diff --git a/variants/norm_annot.sh b/variants/norm_annot.sh
index 776c306c6bae5c965e07f648b16ecf1554e14194..445ceab10508e20aab09264fd5aa3aa57af952a7 100755
--- a/variants/norm_annot.sh
+++ b/variants/norm_annot.sh
@@ -24,9 +24,10 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
 shift $(($OPTIND -1))
 baseDir="`dirname \"$0\"`"
 
-source /etc/profile.d/modules.sh
-module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q 
-
+if [[ -z $isdocker ]]
+   source /etc/profile.d/modules.sh
+   module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q 
+fi
 if [[ -a "${index_path}/genome.fa" ]]
 then
     reffa="${index_path}/genome.fa"
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index f422e9390bbc4f4373b8409e0d7f1d6b220c8633..1ad18f698d142fad2eb1aa04ef879ff5eb3f5553 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -190,6 +190,7 @@ then
 elif [[ $method == 'itdseek' ]]
 then
     stexe=`which samtools`
+    echo $stexe
     samtools view -@ $NPROC -L ${itdbed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | java -Xmx30g -jar $SNPEFF_HOME/SnpSift.jar filter "( LEN < 10000 )" | bgzip > ${pair_id}.itdseek.vcf.gz
     
     tabix ${pair_id}.itdseek.vcf.gz