Mercurial > repos > davidvanzessen > argalaxy_tools
diff report_clonality/r_wrapper.sh @ 44:1d8728f3ff37 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 08 Dec 2017 05:47:33 -0500 |
| parents | 106275b54470 |
| children | 942eea8359fe |
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--- a/report_clonality/r_wrapper.sh Thu Oct 26 09:58:05 2017 -0400 +++ b/report_clonality/r_wrapper.sh Fri Dec 08 05:47:33 2017 -0500 @@ -81,6 +81,12 @@ CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" CIRCOSDIR="/home/galaxy/Anaconda3/bin" fi + + if [ -d "/media/galaxy/data/other_backup/circos/galaxian-circos//bin" ]; then #hopefully temporary fix #or not #really not + USECIRCOS="yes" + CIRCOSTOOLS="/media/galaxy/data/other_backup/circos/galaxian-circos/tools" + CIRCOSDIR="/media/galaxy/data/other_backup/circos/galaxian-circos/bin" + fi fi echo "Using Circos: $USECIRCOS" @@ -94,7 +100,12 @@ circos_file="$outputDir/${sample}_VJ_circos.txt" echo -e -n "labels$(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 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg @@ -104,6 +115,7 @@ 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/ + sed -i -- 's%/%:%g' $outputDir/circos/cells.txt $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg @@ -111,6 +123,7 @@ 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/ + sed -i -- 's%/%:%g' $outputDir/circos/cells.txt $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg