update module load; platypus update sampleid

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

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 ]

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 

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

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

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"

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