# HG changeset patch
# User geert-vandeweyer
# Date 1392904629 18000
# Node ID 86df3f847a725c7b08a853f6bda052dc787cb82f
# Parent  2936bcb2a3780d13049c182a8812ce987cb52133
Switched to R 3.0.2 from iuc, and moved bedtools to seperate tool_definition

diff -r 2936bcb2a378 -r 86df3f847a72 CoverageReport.pl
--- a/CoverageReport.pl	Mon Feb 17 09:49:16 2014 -0500
+++ b/CoverageReport.pl	Thu Feb 20 08:57:09 2014 -0500
@@ -212,7 +212,7 @@
 print OUT 'boxplot(coverage,range=1.5,main="Target Region Coverage")'."\n";
 print OUT 'graphics.off()'."\n";
 close OUT;
-system("cd $wd/Rout && /usr/bin/Rscript boxplot.R");
+system("cd $wd/Rout && Rscript boxplot.R");
 
 ## global nt coverage plot
 ## use perl to make histogram (lower memory)
@@ -306,7 +306,7 @@
 print OUT 'graphics.off()'."\n";
 
 close OUT;
-system("cd $wd/Rout && /usr/bin/Rscript ntplot.R");
+system("cd $wd/Rout && Rscript ntplot.R");
 ## PRINT TO .TEX FILE
 open OUT, ">>$wd/Report/Report.tex";
 # average coverage overviews
@@ -431,7 +431,7 @@
 			print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
 			print OUT 'graphics.off()'."\n";
 			close OUT;
-			system("cd $wd/Rout && /usr/bin/Rscript barplot.R");
+			system("cd $wd/Rout && Rscript barplot.R");
 			if ($scale == 1) {
 				push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
 			}
@@ -473,7 +473,7 @@
 		print OUT 'abline(h=log10('.$thresh.'),lwd=4,col=rgb(255,0,0,100,maxColorValue=255))'."\n";
 		print OUT 'graphics.off()'."\n";
 		close OUT;
-		system("cd $wd/Rout && /usr/bin/Rscript barplot.R");
+		system("cd $wd/Rout && Rscript barplot.R");
 		if ($scale == 1) {
 			push(@small,'\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$currgroup.'.png}');
 		}
@@ -579,7 +579,7 @@
 		print OUT 'graphics.off()'."\n";
 		close OUT;
 		# run R script
-		system("cd $wd/Rout && /usr/bin/Rscript exonplot.R");
+		system("cd $wd/Rout && Rscript exonplot.R");
 		# Add to .TEX
 		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
 		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
@@ -677,7 +677,7 @@
 		print OUT 'graphics.off()'."\n";
 		close OUT;
 		# run R script
-		system("cd $wd/Rout && /usr/bin/Rscript exonplot.R");
+		system("cd $wd/Rout && Rscript exonplot.R");
 		# Add to .TEX
 		print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n";
 		print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n";
diff -r 2936bcb2a378 -r 86df3f847a72 CoverageReport.xml
--- a/CoverageReport.xml	Mon Feb 17 09:49:16 2014 -0500
+++ b/CoverageReport.xml	Thu Feb 20 08:57:09 2014 -0500
@@ -28,7 +28,7 @@
       #end if
   </command>
   <requirements>
-    <requirement type="package" version="2.11.0">R</requirement>
+    <requirement type="package" version="3.0.2">R</requirement>
     <requirement type="package" version="2.18.2">bedtools</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="binary">pdflatex</requirement>
diff -r 2936bcb2a378 -r 86df3f847a72 readme.rst
--- a/readme.rst	Mon Feb 17 09:49:16 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-Panel Resequencing Report
-=========================
-
-This wrapper was created by Geert Vandeweyer. It is free to use, adapt and redistribute, but  please mention the original source. 
-
-Installation
-============
-
-The recommended installation is by means of the toolshed_.
-
-.. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/coverage_report
-
-
-Samtools, bedtools and R should be installed automatically by galaxy if not yet available. 
-PdfLatex must be installed manually and added to the PATH.
-
-
-History
-=======
-0.0.1 - Initial release, no dependency handling
-0.0.2 - Updated release, following toolshed recommendations.
-
-
diff -r 2936bcb2a378 -r 86df3f847a72 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Feb 17 09:49:16 2014 -0500
+++ b/tool_dependencies.xml	Thu Feb 20 08:57:09 2014 -0500
@@ -1,26 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="2.11.0">
-        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="50f7e1e71271" name="package_r_3_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bedtools" version="2.18.2">
-	<install version="1.0">
-		<actions>
-			<action type="download_by_url" target_filename="bedtools2-2.18.2.tar.gz" >https://github.com/arq5x/bedtools2/archive/v2.18.2.tar.gz</action>
-			<action type="shell_command">make</action>
-			<action type="move_file">
-				<source>bin/</source>	
-				<destination>$INSTALL_DIR/bin</destination>
-			</action>
-			<action type="set_environment">
-				<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-               		</action>
-            	</actions>
-        </install>
-        <readme>
-		Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
-     	</readme>
-   </package>
+	<repository changeset_revision="35905f2ae9f4" name="package_bedtools_2_18_2" owner="geert-vandeweyer" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
    <package name="samtools" version="0.1.18">
 	<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>