# HG changeset patch
# User davidvanzessen
# Date 1560864221 14400
# Node ID efe0a2b5d16332a78981033b377cb45b50a04223
# Parent 9ba44c15cad10296a0303d02f6444b915289b1cd
Uploaded
diff -r 9ba44c15cad1 -r efe0a2b5d163 complete_immunerepertoire.xml
--- a/complete_immunerepertoire.xml Tue Jun 18 05:28:11 2019 -0400
+++ b/complete_immunerepertoire.xml Tue Jun 18 09:23:41 2019 -0400
@@ -7,6 +7,7 @@
r-reshape2
r-lymphclon
circos
+ circos-tools
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50046.ttf
Binary file report_clonality/circos/etc/LTe50046.ttf has changed
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50048.ttf
Binary file report_clonality/circos/etc/LTe50048.ttf has changed
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50050.ttf
Binary file report_clonality/circos/etc/LTe50050.ttf has changed
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/LTe50054.ttf
Binary file report_clonality/circos/etc/LTe50054.ttf has changed
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/pragmata.ttf
Binary file report_clonality/circos/etc/pragmata.ttf has changed
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/circos/etc/wingding.ttf
Binary file report_clonality/circos/etc/wingding.ttf has changed
diff -r 9ba44c15cad1 -r efe0a2b5d163 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh Tue Jun 18 05:28:11 2019 -0400
+++ b/report_clonality/r_wrapper.sh Tue Jun 18 09:23:41 2019 -0400
@@ -59,34 +59,12 @@
echo "Report on:" >> $outputFile
mkdir $outputDir/circos
-cp $dir/circos/* $outputDir/circos/
-#CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
-#CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
-
-#CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
-#CIRCOSDIR="/home/galaxy/Anaconda3/bin"
+cp -R $dir/circos/* $outputDir/circos/
USECIRCOS="no"
-if [ -d "$CIRCOSDIR" ]; then
+path_to_circos=$(which circos)
+if [ -x "$path_to_circos" ]; then
USECIRCOS="yes"
-else
- if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix
- USECIRCOS="yes"
- CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
- CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
- fi
-
- if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix #or not
- USECIRCOS="yes"
- 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"
@@ -102,12 +80,12 @@
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 $outputDir/circos/
+ echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/"
+ cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
echo "Circos command:"
- echo "$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1"
- $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
+ echo "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
mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
@@ -116,18 +94,18 @@
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 $outputDir/circos/
+ cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
- $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
+ 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
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 $outputDir/circos/
+ cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
- $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
+ 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
fi