| Previous changeset 10:1400dbec671f (2014-02-14) Next changeset 12:86df3f847a72 (2014-02-20) |
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Commit message:
Hard Coded to use /usr/bin/Rscript instead of dependency one. Will revert when X11 issue is resolved. |
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modified:
CoverageReport.pl |
| b |
| diff -r 1400dbec671f -r 2936bcb2a378 CoverageReport.pl --- a/CoverageReport.pl Fri Feb 14 07:57:17 2014 -0500 +++ b/CoverageReport.pl Mon Feb 17 09:49:16 2014 -0500 |
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| @@ -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 && Rscript boxplot.R"); +system("cd $wd/Rout && /usr/bin/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 && Rscript ntplot.R"); +system("cd $wd/Rout && /usr/bin/Rscript ntplot.R"); ## PRINT TO .TEX FILE open OUT, ">>$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 && Rscript barplot.R"); + system("cd $wd/Rout && /usr/bin/Rscript barplot.R"); if ($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 && Rscript barplot.R"); + system("cd $wd/Rout && /usr/bin/Rscript barplot.R"); if ($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 && Rscript exonplot.R"); + system("cd $wd/Rout && /usr/bin/Rscript exonplot.R"); # Add to .TEX print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n"; print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n"; @@ -677,7 +677,7 @@ print OUT 'graphics.off()'."\n"; close OUT; # run R script - system("cd $wd/Rout && Rscript exonplot.R"); + system("cd $wd/Rout && /usr/bin/Rscript exonplot.R"); # Add to .TEX print TEX '\begin{minipage}{0.5\linewidth}\centering'."\n"; print TEX '\includegraphics[width=\textwidth,keepaspectratio=true]{../Plots/Coverage_'.$exonstr.'.png}'."\n"; |