Mercurial > repos > stef > falco
diff falco-report.sh @ 25:2210b89487c6 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 10 Oct 2014 06:13:06 -0400 |
| parents | |
| children | f1b32c09deaf |
line wrap: on
line diff
--- /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 "<!DOCTYPE html>" >> $html_out +echo "<html>" >> $html_out +echo "<head>" >> $html_out +echo "<style>" >> $html_out +echo " body{ padding: 0px 20px; }" >> $html_out +echo " h1{ color: red; }" >> $html_out +echo " table{ border: 1px solid black; padding: 5px }" >> $html_out +echo "</style>" >> $html_out +echo "</head>" >> $html_out +echo "<body>" >> $html_out +echo " <h1>FALCO</h1>" >> $html_out +echo " <a href=\"index.html\">HTML</a>" >> $html_out +echo " <table><tbody>" >> $html_out +#for file in *.vcf *.txt *.tsv +for file in * +do + lineCount=`wc -l $file | cut -f 1 -d " "` + echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out + #echo " <tr><td> HEAD: " `head $file` "</td></tr>" >> $html_out +done +echo " </tbody></table>" >> $html_out +echo "</body>" >> $html_out +echo "</html>" >> $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