Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 46:fee06348bfad draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 27 Jan 2016 08:39:16 -0500 |
| parents | ee7209928db8 |
| children | d97e1421aa86 |
| files | report_clonality/r_wrapper.sh |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/report_clonality/r_wrapper.sh Wed Jan 27 05:35:55 2016 -0500 +++ b/report_clonality/r_wrapper.sh Wed Jan 27 08:39:16 2016 -0500 @@ -57,18 +57,18 @@ if [ -d "$CIRCOSDIR" ]; then USECIRCOS="yes" fi +echo "Using Circos: $USECIRCOS" sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf for sample in $samples; do #output the samples to a file and create the circos plots with the R script output echo " $sample" >> $outputFile - if [[ "$USECIRCOS" == "no" ]]; then + if [[ "$USECIRCOS" != "yes" ]]; then continue fi circos_file="$outputDir/${sample}_VJ_circos.txt" echo -e -n "labels$(cat ${circos_file})" > ${circos_file} cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ - #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png @@ -127,7 +127,7 @@ #circos -if [[ "$USECIRCOS" == "no" ]]; then +if [[ "$USECIRCOS" == "yes" ]]; then echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile for sample in $samples; do