Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 44:4c5033eb708f draft

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Uploaded
author davidvanzessen
date Tue, 26 Jan 2016 10:10:04 -0500
parents 4d201d22633d
children ee7209928db8
files report_clonality/r_wrapper.sh tool_dependencies.xml
diffstat 2 files changed, 12 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/report_clonality/r_wrapper.sh	Tue Jan 26 07:59:32 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Tue Jan 26 10:10:04 2016 -0500
@@ -31,7 +31,7 @@
 cp $dir/script.js $outputDir
 cp $dir/jquery-1.11.0.min.js $outputDir
 samples=`cat $outputDir/samples.txt`
-#CIRCOSTOOLS="/home/galaxy/Downloads/circos-master/tools"
+
 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2
 echo "<table border = 1>" >> $2
 echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
@@ -51,29 +51,31 @@
 
 mkdir $outputDir/circos
 cp $dir/circos/* $outputDir/circos/
+CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
+CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
 	echo " $sample" >> $outputFile
 	
 	circos_file="$outputDir/${sample}_VJ_circos.txt"
 	echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
-	cat "${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 $outputDir/circos/
+	cat "${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
-	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
 	
 	
 	if [[ "$useD" == "true" ]] ; then
 		circos_file="$outputDir/${sample}_VD_circos.txt"
 		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
-		cat "${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 $outputDir/circos/circos.conf 2>&1
+		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
+		$CIRCOSDIR/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/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 $outputDir/circos/circos.conf 2>&1
+		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
+		$CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
 		mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
 		
 	fi
--- a/tool_dependencies.xml	Tue Jan 26 07:59:32 2016 -0500
+++ b/tool_dependencies.xml	Tue Jan 26 10:10:04 2016 -0500
@@ -28,7 +28,9 @@
     <package name="weblogo" version="3.3">
       <repository changeset_revision="18cb94906560" name="package_weblogo_3_3" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <!--
     <package name="circostools" version="0.20">
-      <repository changeset_revision="ed41baa6271e" name="package_circostools_0_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository name="package_circostools_0_20" owner="iuc" />
     </package>
+    -->
 </tool_dependency>