Mercurial > repos > stef > falco
diff falco-call.sh @ 39:a793ffd0cd04 draft
Uploaded
| author | stef |
|---|---|
| date | Tue, 23 Dec 2014 11:26:33 -0500 |
| parents | f1b32c09deaf |
| children | b4e2b4efae61 |
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--- a/falco-call.sh Fri Oct 10 11:28:57 2014 -0400 +++ b/falco-call.sh Tue Dec 23 11:26:33 2014 -0500 @@ -1,7 +1,7 @@ #!/bin/bash TOOLDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -echo "Start falco sh" +echo "Started FALCO calling" ## ---------- ## Variables setup @@ -13,105 +13,51 @@ ## ---------- ## Create extra init script ## ---------- -if [ $design_file != 'None' ] # Galaxy default is "None" +if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default somehow is "None" then - BED_PATH=$design_file + FILTER_PARAM=" --filter "$filter_file else - BED_PATH="$TOOLDIR/tool-data/GALAXY_TSACP.bed" -fi - -if [ $manifest_file != 'None' ] # Galaxy default is "None" -then - MAN_PATH=$manifest_file -else - MAN_PATH="$TOOLDIR/tool-data/GALAXY_TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt" + FILTER_PARAM="" fi -echo "BED:"$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 +if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" +then + MANIFEST_PARAM=" --manifest "$manifest_file +else + MANIFEST_PARAM="" +fi ## ---------- ## 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 - - - +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 -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 ./ ./ - +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" ## ---------- @@ -128,14 +74,15 @@ echo "</head>" >> $html_out echo "<body>" >> $html_out echo " <h1>FALCO</h1>" >> $html_out -echo " <a href=\"index.html\">HTML</a>" >> $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 *.tsv -for file in * +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: " `head $file` "</td></tr>" >> $html_out + echo " <tr><td> --> " `head -1 $file` "</td></tr>" >> $html_out done echo " </tbody></table>" >> $html_out echo "</body>" >> $html_out @@ -146,14 +93,14 @@ ## ---------- #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 +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 *.tsv $out_path; cp *.txt $out_path; cp *.html $out_path +cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path ## ---------- echo "END falco sh"