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author stef
date Fri, 10 Oct 2014 10:13:55 -0400
parents 12f7ce7de71f
children f1b32c09deaf
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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

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
## ----------
echo "Starting VcAn"

## DEBUG
#exit 0

$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