| Previous changeset 44:1d8728f3ff37 (2017-12-08) Next changeset 46:4d2a8f98a502 (2019-01-28) |
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Commit message:
Uploaded |
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modified:
report_clonality/r_wrapper.sh |
| b |
| diff -r 1d8728f3ff37 -r 942eea8359fe report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Fri Dec 08 05:47:33 2017 -0500 +++ b/report_clonality/r_wrapper.sh Fri Dec 08 06:32:16 2017 -0500 |
| [ |
| @@ -99,11 +99,12 @@ fi circos_file="$outputDir/${sample}_VJ_circos.txt" + sed -i -- 's%/%:%g' $circos_file echo -e -n "labels$(cat ${circos_file})" > ${circos_file} echo "Circos tools command:" echo "cat \"${circos_file}\" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/" cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/ - sed -i -- 's%/%:%g' $outputDir/circos/cells.txt + echo "Circos command:" echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1" $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 @@ -113,6 +114,7 @@ if [[ "$useD" == "true" ]] ; then circos_file="$outputDir/${sample}_VD_circos.txt" + sed -i -- 's%/%:%g' $circos_file echo -e -n "labels$(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/ sed -i -- 's%/%:%g' $outputDir/circos/cells.txt @@ -121,6 +123,7 @@ mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg circos_file="$outputDir/${sample}_DJ_circos.txt" + sed -i -- 's%/%:%g' $circos_file echo -e -n "labels$(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/ sed -i -- 's%/%:%g' $outputDir/circos/cells.txt |