Mercurial > repos > geert-vandeweyer > coverage_report
changeset 12:86df3f847a72 draft
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 | a030e3cd3da5 |
| files | CoverageReport.pl CoverageReport.xml readme.rst tool_dependencies.xml |
| diffstat | 4 files changed, 10 insertions(+), 48 deletions(-) [+] |
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--- 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";
--- 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>
--- 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. - -
--- 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>