# HG changeset patch # User stef # Date 1412935986 14400 # Node ID 2210b89487c6743c37be97d7fd41c3b618c18665 # Parent 4b4fba5eab4df8745983716568a55e326d763497 Uploaded diff -r 4b4fba5eab4d -r 2210b89487c6 falco-call.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco-call.sh Fri Oct 10 06:13:06 2014 -0400 @@ -0,0 +1,148 @@ +#!/bin/bash +TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +echo "Start falco sh" + +## ---------- +## Variables setup +## ---------- +source $1 + +bam_base=`echo $bam_name | sed 's#.bam$##' - ` + +## ---------- +## Create extra init script +## ---------- +if [ $design_file != 'None' ] # Galaxy default is "None" +then + BED_PATH=$design_file +else + BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" +fi + +if [ $manifest_file != 'None' ] # Galaxy default is "None" +then + MAN_PATH=$manifest_file +else + MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" +fi + +echo "BED:"$design_file +echo "MAN:"$manifest_file +echo "BED chosen:"$BED_PATH +echo "MAN chosen:"$MAN_PATH +#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH +#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH + +init_file="galaxy_init.sh" +echo '#!/bin/bash' > $init_file + +## executables +#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file +#echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file +#echo "snpSift=/ccagc/lib/SnpSift" >> $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" >> $init_file + +## files +echo "targetBed=$BED_PATH" >> $init_file +echo "manifest=$MAN_PATH" >> $init_file + +## ---------- +## Status / debug +## ---------- +echo "BAM: "$bam_file +echo "OUT: "$bam_name +echo "BAMBASE: "$bam_base +#echo "OUTPATH: "$out_path +#echo "HTMLOUT: "$html_out +echo "VCFOUT : "$vcf_out +echo "INIT : "$init_file + +source $init_file + +echo "--- sam ---" +samtools +#echo "--- bcf ---" +#bcftools +#echo "--- snpsift ---" +#java -jar $snpSift/SnpSift.jar +#echo "--- snpeff ---" +#java -jar $snpEff/snpeff.jar +#echo "--- varscan ---" +#java -jar $varScan + +exit 0 + +## ---------- +## create output files dir +## ---------- +mkdir $out_path +mkdir $out_path/$bam_base + +## ---------- +## running analysis +## ---------- +echo "Starting VcAn" +$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base +#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more + +#echo "Starting amplicon-Report" +#$TOOLDIR/falco/amplicon-Report.sh $bam_base + +#echo "Starting QC" +#$TOOLDIR/falco/amplicon-QC.sh $bam_file + +#echo "Starting plots.R" +#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf + +#echo "Starting mkHtmlReport" +#$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./ + + + +## ---------- +## 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 + +## ---------- +## creating galaxy history outputs +## ---------- +#cp 'index.html' $html_out # this is the overview of samples html +#cp $bam_base'.html' $out_path/'out.html' # this is the sample html +cp $bam_base'.vcf' $vcf_out + +## ---------- +## copy files to keep to output path +## ---------- +#cp -r ./$bam_base/*png $out_path/$bam_base/ +#cp -r ./* $out_path +#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path + +## ---------- +echo "END falco sh" +exit 0 \ No newline at end of file diff -r 4b4fba5eab4d -r 2210b89487c6 falco-call.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco-call.xml Fri Oct 10 06:13:06 2014 -0400 @@ -0,0 +1,137 @@ + + + + + samtools + + R + + + TOOL_DIR + + + + FALCO: Amplicon Analysis Pipeline + + + + + + + + + falco-call.sh $falco_cfg; + + + + + + + + + + + + + + + \S+ + + + + + + + + + + + + + + + + + + + design_file=$design_file + manifest_file=$manifest_file + bam_file=$bam + bam_name=$bam.name + + vcf_out=$vcf_output + out_path=${vcf_output.files_path} + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**Introduction** + +This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_ + +.. _FALCO: https://bitbucket.org/daoud/falco + +Calls and annotates genomic variants for each amplicon in a design. + +----- + +**Citation** + +For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). + + + + diff -r 4b4fba5eab4d -r 2210b89487c6 falco-report.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco-report.sh Fri Oct 10 06:13:06 2014 -0400 @@ -0,0 +1,159 @@ +#!/bin/bash +TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +echo "Start falco sh" + +## ---------- +## Variables setup +## ---------- +#bam_file=$1 +#bam_name=$2 +#html_out=$3 +#vcf_out=$4 +#out_path=$5 +source $1 +JAR_PATH=$2 +#JAR_PATH=$3 + +bam_base=`echo $bam_name | sed 's#.bam$##' - ` + +## ---------- +## Create extra init script +## ---------- +#if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi +#if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi +if [ $design_file != 'None' ] # Galaxy default is "None" +then + BED_PATH=$design_file +else + BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" +fi + +if [ $manifest_file != 'None' ] # Galaxy default is "None" +then + MAN_PATH=$manifest_file +else + MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" +fi + +echo "BED:"$design_file +echo "MAN:"$manifest_file +echo "BED chosen:"$BED_PATH +echo "MAN chosen:"$MAN_PATH +#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH +#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH +echo "JAR_PATH1:"$JAR_PATH +#echo "JAR_PATH2:"$jar_path2 + +init_file="galaxy_init.sh" +echo '#!/bin/bash' > $init_file + +## executables +#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file +echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file +#echo "snpSift=/ccagc/lib/SnpSift" >> $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" >> $init_file + +## files +echo "targetBed=$BED_PATH" >> $init_file +echo "manifest=$MAN_PATH" >> $init_file + +## ---------- +## Status / debug +## ---------- +echo "BAM: "$bam_file +echo "OUT: "$bam_name +echo "BAMBASE: "$bam_base +echo "OUTPATH: "$out_path +echo "HTMLOUT: "$html_out +echo "VCFOUT : "$vcf_out +echo "INIT : "$init_file + +source $init_file + +echo "--- sam ---" +samtools +echo "--- bcf ---" +bcftools +echo "--- snpsift ---" +java -jar $snpSift/SnpSift.jar +echo "--- snpeff ---" +java -jar $snpEff/snpeff.jar +echo "--- varscan ---" +java -jar $varScan + +exit 0 + +## ---------- +## create output files dir +## ---------- +mkdir $out_path +mkdir $out_path/$bam_base + +## ---------- +## running analysis +## ---------- +echo "Starting VcAn" +$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base +#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more + +echo "Starting amplicon-Report" +$TOOLDIR/falco/amplicon-Report.sh $bam_base + +echo "Starting QC" +$TOOLDIR/falco/amplicon-QC.sh $bam_file + +#echo "Starting plots.R" +#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf + +echo "Starting mkHtmlReport" +$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./ + + + +## ---------- +## 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 + +## ---------- +## creating galaxy history outputs +## ---------- +#cp 'index.html' $html_out # this is the overview of samples html +cp $bam_base'.html' $out_path/'out.html' # this is the sample html +cp $bam_base'.vcf' $vcf_out + +## ---------- +## copy files to keep to output path +## ---------- +cp -r ./$bam_base/*png $out_path/$bam_base/ +cp -r ./* $out_path +#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path + +## ---------- +echo "END falco sh" +exit 0 \ No newline at end of file diff -r 4b4fba5eab4d -r 2210b89487c6 falco-report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco-report.xml Fri Oct 10 06:13:06 2014 -0400 @@ -0,0 +1,137 @@ + + + + + samtools + + R + + + TOOL_DIR + + + + FALCO: Amplicon Analysis Pipeline + + + + + + + + + falco-report.sh $falco_cfg; + + + + + + + + + + + + + + + \S+ + + + + + + + + + + + + + + + + + + + design_file=$design_file + manifest_file=$manifest_file + bam_file=$bam + bam_name=$bam.name + + vcf_out=$vcf_output + out_path=${vcf_output.files_path} + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**Introduction** + +This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_ + +.. _FALCO: https://bitbucket.org/daoud/falco + +Calls and annotates genomic variants for each amplicon in a design. + +----- + +**Citation** + +For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). + + + + diff -r 4b4fba5eab4d -r 2210b89487c6 falco.sh --- a/falco.sh Wed Oct 08 08:14:41 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,159 +0,0 @@ -#!/bin/bash -TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" - -echo "Start falco sh" - -## ---------- -## Variables setup -## ---------- -#bam_file=$1 -#bam_name=$2 -#html_out=$3 -#vcf_out=$4 -#out_path=$5 -source $1 -JAR_PATH=$2 -#JAR_PATH=$3 - -bam_base=`echo $bam_name | sed 's#.bam$##' - ` - -## ---------- -## Create extra init script -## ---------- -#if [ $design_file != 'None' && $design_file != '' ]; then BED_PATH=$design_file; fi -#if [ $manifest_file != 'None' && $manifest_file != '' ]; then MAN_PATH=$manifest_file; fi -if [ $design_file != 'None' ] # Galaxy default is "None" -then - BED_PATH=$design_file -else - BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" -fi - -if [ $manifest_file != 'None' ] # Galaxy default is "None" -then - MAN_PATH=$manifest_file -else - MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" -fi - -echo "BED:"$design_file -echo "MAN:"$manifest_file -echo "BED chosen:"$BED_PATH -echo "MAN chosen:"$MAN_PATH -#echo "VARSCAN_PATH1:"$SNPEFF_JAR_PATH -#echo "VARSCAN_PATH2:"\$SNPEFF_JAR_PATH -echo "JAR_PATH1:"$JAR_PATH -#echo "JAR_PATH2:"$jar_path2 - -init_file="galaxy_init.sh" -echo '#!/bin/bash' > $init_file - -## executables -#echo "snpEff=/ccagc/lib/snpEff/snpEff_v3_4" >> $init_file -echo "snpEff=\$SNPEFF_JAR_PATH/" >> $init_file -#echo "snpSift=/ccagc/lib/SnpSift" >> $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" >> $init_file - -## files -echo "targetBed=$BED_PATH" >> $init_file -echo "manifest=$MAN_PATH" >> $init_file - -## ---------- -## Status / debug -## ---------- -echo "BAM: "$bam_file -echo "OUT: "$bam_name -echo "BAMBASE: "$bam_base -echo "OUTPATH: "$out_path -echo "HTMLOUT: "$html_out -echo "VCFOUT : "$vcf_out -echo "INIT : "$init_file - -source $init_file - -echo "--- sam ---" -samtools -echo "--- bcf ---" -bcftools -echo "--- snpsift ---" -java -jar $snpSift/SnpSift.jar -echo "--- snpeff ---" -java -jar $snpEff/snpeff.jar -echo "--- varscan ---" -java -jar $varScan - -exit 0 - -## ---------- -## create output files dir -## ---------- -mkdir $out_path -mkdir $out_path/$bam_base - -## ---------- -## running analysis -## ---------- -echo "Starting VcAn" -$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base -#$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more - -echo "Starting amplicon-Report" -$TOOLDIR/falco/amplicon-Report.sh $bam_base - -echo "Starting QC" -$TOOLDIR/falco/amplicon-QC.sh $bam_file - -#echo "Starting plots.R" -#$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf - -echo "Starting mkHtmlReport" -$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./ - - - -## ---------- -## 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 - -## ---------- -## creating galaxy history outputs -## ---------- -#cp 'index.html' $html_out # this is the overview of samples html -cp $bam_base'.html' $out_path/'out.html' # this is the sample html -cp $bam_base'.vcf' $vcf_out - -## ---------- -## copy files to keep to output path -## ---------- -cp -r ./$bam_base/*png $out_path/$bam_base/ -cp -r ./* $out_path -#cp *.vcf $out_path; cp *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path - -## ---------- -echo "END falco sh" -exit 0 \ No newline at end of file diff -r 4b4fba5eab4d -r 2210b89487c6 falco.xml --- a/falco.xml Wed Oct 08 08:14:41 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ - - - - - samtools - R - snpeff - varscan - bcftools - - JAR_PATH1 - JAR_PATH2 - TOOL_DIR - - - FALCO: Amplicon Analysis Pipeline - - - - - - - - - falco.sh $falco_cfg \$SNPEFF_JAR_PATH; - - - - - - - - - - - - - - - \S+ - - - - - - - - - - - - - - - - - - - design_file=$design_file - manifest_file=$manifest_file - bam_file=$bam - bam_name=$bam.name - html_out=$html_output - vcf_out=$vcf_output - out_path=${html_output.files_path} - - - - - - - - - - - - - - - - - - -.. class:: infomark - -**Introduction** - -This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_ - -.. _FALCO: https://bitbucket.org/daoud/falco - -Calls and annotates genomic variants for each amplicon in a design. - ------ - -**Citation** - -For the underlying tool please cite: Daoud Sie et al. Title TBA (submitted). - - - - diff -r 4b4fba5eab4d -r 2210b89487c6 tool_dependencies.xml --- a/tool_dependencies.xml Wed Oct 08 08:14:41 2014 -0400 +++ b/tool_dependencies.xml Fri Oct 10 06:13:06 2014 -0400 @@ -2,42 +2,45 @@ - - - Let's see where this msg appears...R + + - Let's see where this msg appears...samtools + + $REPOSITORY_INSTALL_DIR + +