Mercurial > repos > davidvanzessen > argalaxy_tools

diff report_clonality/r_wrapper.sh @ 44:1d8728f3ff37 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Fri, 08 Dec 2017 05:47:33 -0500
parents 106275b54470
children 942eea8359fe
line wrap: on
line diff
--- 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