Mercurial > repos > stef > falco
view falco-call.sh @ 38:f1b32c09deaf draft
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author | stef |
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date | Fri, 10 Oct 2014 11:28:57 -0400 |
parents | 12f7ce7de71f |
children | a793ffd0cd04 |
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#!/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 echo "samtools=samtools" >> $init_file echo "bcftools=bcftools" >> $init_file ## files echo "targetBed=$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 echo "------ sourcing init_file" source $init_file #echo "------ --- ------" #echo "------ sam ------" #echo "------ --- ------" #$samtools #echo "------ --- ------" #echo "------ bcf ------" #echo "------ --- ------" #$bcftools #echo "--- snpsift ---" #java -jar $snpSift/SnpSift.jar #echo "--- snpeff ---" #java -jar $snpEff/snpeff.jar #echo "--- varscan ---" #java -jar $varScan ## ---------- ## create output files dir ## ---------- mkdir $out_path mkdir $out_path/$bam_base ## ---------- ## running analysis ## ---------- ## 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 #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