Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 42:65134a538c5a draft
Uploaded
author | davidvanzessen |
---|---|
date | Tue, 26 Jan 2016 03:07:39 -0500 |
parents | 85566b336a72 |
children | 4d201d22633d |
files | report_clonality/r_wrapper.sh |
diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/report_clonality/r_wrapper.sh Tue Jan 26 03:01:48 2016 -0500 +++ b/report_clonality/r_wrapper.sh Tue Jan 26 03:07:39 2016 -0500 @@ -57,7 +57,7 @@ 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 $outputDir/circos/ + cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/ #/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png @@ -66,14 +66,14 @@ if [[ "$useD" == "true" ]] ; then circos_file="$outputDir/${sample}_VD_circos.txt" echo -e -n "labels$(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 $outputDir/circos/circos.conf 2>&1 + cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/ + circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png 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/ - /home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1 + cat "${circos_file}" | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/circos-tools-0.20/tools/tableviewer/bin/make-conf -dir $outputDir/circos/ + circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png fi