# HG changeset patch # User stef # Date 1412954937 14400 # Node ID f1b32c09deafc1f81a9d845e8226d5e68e48d258 # Parent eb9a8e3a36820c90867fb351494f9aa384f711f0 Uploaded diff -r eb9a8e3a3682 -r f1b32c09deaf falco-call.sh --- a/falco-call.sh Fri Oct 10 11:07:36 2014 -0400 +++ b/falco-call.sh Fri Oct 10 11:28:57 2014 -0400 @@ -62,16 +62,17 @@ echo "VCFOUT : "$vcf_out echo "INIT : "$init_file +echo "------ sourcing init_file" source $init_file -echo "------ --- ------" -echo "------ sam ------" -echo "------ --- ------" -$samtools -echo "------ --- ------" -echo "------ bcf ------" -echo "------ --- ------" -$bcftools +#echo "------ --- ------" +#echo "------ sam ------" +#echo "------ --- ------" +#$samtools +#echo "------ --- ------" +#echo "------ bcf ------" +#echo "------ --- ------" +#$bcftools #echo "--- snpsift ---" #java -jar $snpSift/SnpSift.jar #echo "--- snpeff ---" @@ -85,17 +86,16 @@ ## ---------- ## create output files dir ## ---------- -#mkdir $out_path -#mkdir $out_path/$bam_base +mkdir $out_path +mkdir $out_path/$bam_base ## ---------- ## running analysis ## ---------- -echo "Starting VcAn" ## DEBUG #exit 0 - +echo "Starting VcAn" $TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base echo "...done with VcAn" #$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more @@ -117,29 +117,29 @@ ## ---------- ## create index html for main galaxy output ## ---------- -# echo "" >> $html_out -# echo "" >> $html_out -# echo "" >> $html_out -# echo "" >> $html_out -# echo "" >> $html_out -# echo "" >> $html_out -# echo "

FALCO

" >> $html_out -# echo " HTML" >> $html_out -# echo " " >> $html_out -# #for file in *.vcf *.txt *.tsv -# for file in * -# do -# lineCount=`wc -l $file | cut -f 1 -d " "` -# echo " " >> $html_out -# #echo " " >> $html_out -# done -# echo "

$file has $lineCount lines

HEAD: " `head $file` "

" >> $html_out -# echo "" >> $html_out -# echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "" >> $html_out +echo "

FALCO

" >> $html_out +echo " HTML" >> $html_out +echo " " >> $html_out +#for file in *.vcf *.txt *.tsv +for file in * +do + lineCount=`wc -l $file | cut -f 1 -d " "` + echo " " >> $html_out + #echo " " >> $html_out +done +echo "

$file has $lineCount lines

HEAD: " `head $file` "

" >> $html_out +echo "" >> $html_out +echo "" >> $html_out ## ---------- ## creating galaxy history outputs diff -r eb9a8e3a3682 -r f1b32c09deaf falco-call.xml --- a/falco-call.xml Fri Oct 10 11:07:36 2014 -0400 +++ b/falco-call.xml Fri Oct 10 11:28:57 2014 -0400 @@ -83,7 +83,7 @@ manifest_file=$manifest_file bam_file=$bam bam_name=$bam.name - + html_out=$html_output vcf_out=$vcf_output out_path=${vcf_output.files_path} @@ -98,7 +98,7 @@ - + diff -r eb9a8e3a3682 -r f1b32c09deaf falco-report.sh --- a/falco-report.sh Fri Oct 10 11:07:36 2014 -0400 +++ b/falco-report.sh Fri Oct 10 11:28:57 2014 -0400 @@ -12,7 +12,6 @@ #vcf_out=$4 #out_path=$5 source $1 -JAR_PATH=$2 #JAR_PATH=$3 bam_base=`echo $bam_name | sed 's#.bam$##' - ` @@ -50,11 +49,11 @@ ## executables #echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file -echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file +#echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file #echo "snpSift=/ccagc/lib/SnpSift" >> $init_file -echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file +#echo "snpSift=\$SNPEFF_JAR_PATH/" >> $init_file #echo "varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar" >> $init_file -echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file +#echo "varscan=\$JAVA_JAR_PATH/VarScan.v2.3.5.jar" >> $init_file ## files echo "targetBed=$BED_PATH" >> $init_file @@ -77,12 +76,12 @@ samtools echo "--- bcf ---" bcftools -echo "--- snpsift ---" -java -jar $snpSift/SnpSift.jar -echo "--- snpeff ---" -java -jar $snpEff/snpeff.jar -echo "--- varscan ---" -java -jar $varScan +#echo "--- snpsift ---" +#java -jar $snpSift/SnpSift.jar +#echo "--- snpeff ---" +#java -jar $snpEff/snpeff.jar +#echo "--- varscan ---" +#java -jar $varScan exit 0 diff -r eb9a8e3a3682 -r f1b32c09deaf falco/amplicon-VcAn-TSACP.sh diff -r eb9a8e3a3682 -r f1b32c09deaf falco/init.sh --- a/falco/init.sh Fri Oct 10 11:07:36 2014 -0400 +++ b/falco/init.sh Fri Oct 10 11:28:57 2014 -0400 @@ -2,37 +2,37 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -#index=/ccagc/data/ref/hg19/stampy/hg19 -#hash=/ccagc/data/ref/hg19/stampy/hg19 -#faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -#bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa +index=/ccagc/data/ref/hg19/stampy/hg19 +hash=/ccagc/data/ref/hg19/stampy/hg19 +faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa +bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa #manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt #targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed -#dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf -#dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt -#clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf -#cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf -#cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf -#locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv -#canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv +dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf +dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt +clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf +cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf +cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf +locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv +canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" -#adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt -#qTrim=/ccagc/bin/fastq_quality_trimmer -#stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py +adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt +qTrim=/ccagc/bin/fastq_quality_trimmer +stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py #samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools #bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools -#snpEff=/ccagc/lib/snpEff/snpEff_3_0a -#snpEff=/ccagc/lib/snpEff/snpEff_v3_4 -#snpSift=/ccagc/lib/SnpSift +snpEff=/ccagc/lib/snpEff/snpEff_3_0a +snpEff=/ccagc/lib/snpEff/snpEff_v3_4 +snpSift=/ccagc/lib/SnpSift -#varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar -#java=/usr/bin/java -#bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa -#flash=/ccagc/lib/flash/FLASH-1.2.2/flash +varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar +java=/usr/bin/java +bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa +flash=/ccagc/lib/flash/FLASH-1.2.2/flash pairUp=$DIR/misc/pairUp.pl pileup2cov=$DIR/misc/pileup2cov.pl diff -r eb9a8e3a3682 -r f1b32c09deaf falco/misc/amplicon-VcAn-TSACP.sh --- a/falco/misc/amplicon-VcAn-TSACP.sh Fri Oct 10 11:07:36 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -source $DIR/init.sh - -TMP=./tmp -if [ ! -e $TMP ] -then - mkdir $TMP -fi - -bam=$1 -output=$2 - -if [ ! -e $output.vcf ] -then -# Use Extended BAQ! -# Tweak indel settings -m and -F -echo `date` " [$$] - $samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | bcftools view -bvcg - > $output.bcf" -$samtools mpileup -Euf $faref -L 1000000 -d 1000000 -m 150 -F 0.01 -o 20 $bam | $bcftools view -bvcg - > $output.bcf -echo `date` " [$$] - Done!" -echo `date` " [$$] - bcftools view $output.bcf > $output.vcf" -$bcftools view $output.bcf > $output.vcf -echo `date` " [$$] - Done!" -fi - -# Annotation -#VcfIn=$output.vcf -#VcfOut=$output.samtools.vcf - -#if [ ! -e $VcfOut ] -#then -# Samtools annotation -#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -#mv $output.snpeff.2.vcf $VcfOut -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -#echo `date` " [$$] - Done!" -#fi - -if [ ! -e $output.qc.ann.txt ] -then -echo `date` " [$$] - $pileup2cov2 $bam $faref $manifest $output $samtools" -$pileup2cov2 $bam $faref $manifest $output $samtools -echo `date` " [$$] - Done!" -fi - -if [ ! -e $output.qc.ann.qual.txt ] -then -echo `date` " [$$] - RScript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt" -Rscript $addQual $output.qc.ann.txt $output.qc.ann.qual.txt $DIR/misc/func.R $locifilt -echo `date` " [$$] - Done!" -fi - -echo `date` " [$$] - $qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output" -$qcFilt $output.qc.ann.qual.txt $clinvar $cosmic $cosmicNC $output -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf" -$qc2vcf $output.qc.ann.qual.filt.txt > $output.qc.ann.filt.vcf -echo `date` " [$$] - Done!" - -echo `date` " [$$] - $qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf" -$qc2vcf $output.qc.ann.qual.clinvar.txt > $output.qc.ann.clinvar.vcf -echo `date` " [$$] - Done!" - - - -#VcfIn=$output.qc.ann.filt.vcf -#VcfOut=$output.qc.ann.filt.a.vcf - -#if [ ! -e $VcfOut ] -#then - -# qc vcf annotation -#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -#mv $output.snpeff.2.vcf $VcfOut -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -#echo `date` " [$$] - Done!" -#fi - -#VcfIn=$output.qc.ann.clinvar.vcf -# VcfOut=$output.qc.ann.clinvar.a.vcf - -#if [ ! -e $VcfOut ] -#then - -# qc vcf annotation -#echo `date` " [$$] - $java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > tmp.snpeff.vcf" -#$java -jar $snpEff/snpEff.jar eff hg19 -noStats -noLog -o vcf -c $snpEff/snpEff.config $VcfIn > $output.snpeff.vcf -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf" -#$java -jar $snpSift/SnpSift_latest.jar annotate -v $dbSnp $output.snpeff.vcf > $output.snpeff.2.vcf -#mv $output.snpeff.2.vcf $VcfOut -#echo `date` " [$$] - Done!" - -#echo `date` " [$$] - $java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf" -#$java -jar /opt/SnpSift/SnpSift_latest.jar dbnsfp -v $dbNSFP $output.snpeff.2.vcf > $output.snpeff.3.vcf -#mv $output.snpeff.3.vcf $VcfOut -#echo `date` " [$$] - Done!" -#fi diff -r eb9a8e3a3682 -r f1b32c09deaf falco/misc/init.sh --- a/falco/misc/init.sh Fri Oct 10 11:07:36 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -#!/bin/bash - -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -index=/ccagc/data/ref/hg19/stampy/hg19 -hash=/ccagc/data/ref/hg19/stampy/hg19 -faref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -bwaref=/ccagc/data/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.5.x/genome.fa -#manifest=/ccagc/data/ref/manifests/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt -#targetBed=/ccagc/data/ref/manifests/TSACP/TSACP.bed - -dbSnp=/ccagc/data/ref/dbSNP/common_no_known_medical_impact_00-latest.f.vcf -dbNSFP=/ccagc/data/ref/dbNSFP/dbNSFP2.0b3.txt -clinvar=/ccagc/data/ref/dbSNP/clinvar_00-latest.f.vcf -cosmic=/ccagc/data/ref/cosmic/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf -cosmicNC=/ccagc/data/ref/cosmic/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf -locifilt=/ccagc/data/ref/dbSNP/locifilt.tsv -canonicals=/ccagc/data/ref/manifests/TSACP/canonicals.tsv - -illmP5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" -illmP7="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" - -adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt -qTrim=/ccagc/bin/fastq_quality_trimmer -stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py -#samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools -#bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools -snpEff=/ccagc/lib/snpEff/snpEff_3_0a -snpEff=/ccagc/lib/snpEff/snpEff_v3_4 -snpSift=/ccagc/lib/SnpSift - -varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar -java=/usr/bin/java -bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa -flash=/ccagc/lib/flash/FLASH-1.2.2/flash - -pairUp=$DIR/misc/pairUp.pl -pileup2cov=$DIR/misc/pileup2cov.pl -pileup2cov2=$DIR/misc/perAmpliconAnalysis.pl -addQual=$DIR/misc/addQual.R - -qc2vcf=$DIR/misc/qc2vcf.pl -qcFilt=$DIR/misc/qcFilt.pl -plots=$DIR/misc/plots.R -plotsPng=$DIR/misc/plotsPng.R - -attachManifest=$DIR/misc/attachManifest.pl -plots=$DIR/misc/plots.R -VcAn=$DIR/amplicon-VcAn-TSACP.sh -report=$DIR/amplicon-Report.sh - -alignmentStats=$DIR/misc/alignmentStats.pl -errorRate=$DIR/misc/errorRate.pl -plotQc=$DIR/misc/plotsQC.R - -#export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/ -source ./galaxy_init.sh diff -r eb9a8e3a3682 -r f1b32c09deaf tool_dependencies.xml --- a/tool_dependencies.xml Fri Oct 10 11:07:36 2014 -0400 +++ b/tool_dependencies.xml Fri Oct 10 11:28:57 2014 -0400 @@ -13,7 +13,6 @@ - Let's see where this msg appears...bcftools