Mercurial > repos > geert-vandeweyer > coverage_report

diff CoverageReport.pl @ 12:86df3f847a72 draft

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Switched to R 3.0.2 from iuc, and moved bedtools to seperate tool_definition
author geert-vandeweyer
date Thu, 20 Feb 2014 08:57:09 -0500
parents 2936bcb2a378
children 95062840f80f
line wrap: on
line diff
--- 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";