Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/r_wrapper.sh @ 33:6603110e5be3 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 28 Mar 2017 08:38:58 -0400 |
| parents | 7c33029fd63d |
| children | dc6c53a11d7d |
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--- a/report_clonality/r_wrapper.sh Tue Mar 28 05:40:04 2017 -0400 +++ b/report_clonality/r_wrapper.sh Tue Mar 28 08:38:58 2017 -0400 @@ -93,6 +93,7 @@ cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png + mv $outputDir/circos/circos.pdf $outputDir/circosVJ_${sample}.pdf if [[ "$useD" == "true" ]] ; then @@ -101,13 +102,14 @@ cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png + mv $outputDir/circos/circos.pdf $outputDir/circosVD_${sample}.pdf circos_file="$outputDir/${sample}_DJ_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/ $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png - + mv $outputDir/circos/circos.pdf $outputDir/circosDJ_${sample}.pdf fi done echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile