Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/r_wrapper.sh @ 36:edf2d5882b77 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 28 Mar 2017 08:57:05 -0400 |
| parents | dc6c53a11d7d |
| children | b6936fb52ab9 |
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--- a/report_clonality/r_wrapper.sh Tue Mar 28 08:51:34 2017 -0400 +++ b/report_clonality/r_wrapper.sh Tue Mar 28 08:57:05 2017 -0400 @@ -93,7 +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 + mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg if [[ "$useD" == "true" ]] ; then @@ -102,14 +102,14 @@ cat "${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 + mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg 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 + mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg fi done echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile