| Previous changeset 32:7c33029fd63d (2017-03-28) Next changeset 34:7b8147b61a34 (2017-03-28) |
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Commit message:
Uploaded |
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modified:
report_clonality/circos/circos.conf report_clonality/r_wrapper.sh |
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| diff -r 7c33029fd63d -r 6603110e5be3 report_clonality/circos/circos.conf --- a/report_clonality/circos/circos.conf Tue Mar 28 05:40:04 2017 -0400 +++ b/report_clonality/circos/circos.conf Tue Mar 28 08:38:58 2017 -0400 |
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| @@ -32,7 +32,7 @@ 24bit = yes svg = no png = yes -pdf = no +pdf = yes # radius of inscribed circle in image radius = 1500p background = white |
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| diff -r 7c33029fd63d -r 6603110e5be3 report_clonality/r_wrapper.sh --- 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 |
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| @@ -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 |