Mercurial > repos > stef > falco
view falco-call.sh @ 49:b4e543d81a98 draft
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author | stef |
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date | Tue, 30 Dec 2014 06:27:20 -0500 |
parents | a793ffd0cd04 |
children | b4e2b4efae61 |
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#!/bin/bash TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" echo "Started FALCO calling" ## ---------- ## Variables setup ## ---------- source $1 bam_base=`echo $bam_name | sed 's#.bam$##' - ` ## ---------- ## Create extra init script ## ---------- if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default somehow is "None" then FILTER_PARAM=" --filter "$filter_file else FILTER_PARAM="" fi if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" then MANIFEST_PARAM=" --manifest "$manifest_file else MANIFEST_PARAM="" fi ## ---------- ## Status / debug ## ---------- DEBUG=1 if [ $DEBUG ] then DBS="[INFO] " echo $DBS"FILTER: "$filter_file echo $DBS"MANIFES: "$manifest_file echo $DBS"REFFILE: "$REF_FILE echo $DBS"DB_KEY: "$DB_KEY echo $DBS"REF_SRC: "$REF_SOURCE echo $DBS"BAMFILE: "$bam_file echo $DBS"BAMNAME: "$bam_name echo $DBS"BAMBASE: "$bam_base echo $DBS"OUTPATH: "$out_path fi ## ---------- ## create output files dir ## ---------- mkdir $out_path ## ---------- ## running analysis ## ---------- echo "Starting variant calling" CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM" echo "[INFO] "$CALL_STRING perl $CALL_STRING echo "...done with variant calling" ## ---------- ## 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 " <p>This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)</p>" >> $html_out #echo " <a href=\"index.html\">HTML</a>" >> $html_out echo " <table><tbody>" >> $html_out for file in *.vcf *.txt *stderr *stdout #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 -1 $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'.falco.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 *.txt $out_path; cp *_std* $out_path ## ---------- echo "END falco sh" exit 0