From: Tim Reddy Tim <treddy@hudsonalpha.org>
Date: Mon, 24 Nov 2008 23:29:53 +0000 (+0000)
Subject: Add validation primer code to MACS source
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=30c4f93d015a9fe4c404158097c405ca2496ad1b

Add validation primer code to MACS source
---

diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm
index 3aab29c..9cf527a 100755
--- a/htswanalysis/scripts/ConfigureTasks.pm
+++ b/htswanalysis/scripts/ConfigureTasks.pm
@@ -359,6 +359,7 @@ sub WritePeakCallingTasks {
 
         $cmd .= "\n".$name."_peaks.bed: ".$name."_peaks.xls\n";
         $cmd .= "\t$root_dir/scripts/MACS_2_BED.sh $< $name > $@\n\n"
+        $cmd .= "\t/Library/WebServer/CGI-Executables/ValidationDesign/primer_design_cmd.pm http://m304-apple-server.stanford.edu/Tasks/$task/".$name."_peaks.bed $signal > ValidationPrimers.html\n\n";
 
         $cmd .= "\n".$name."_peaks.tab: ".$name."_peaks.bed\n";
         $cmd .= "\t".'cat $< | awk \'{print NR"\t"$$1"\t"$$2"\t"$$3"\t1"}\' > $@'."\n\n";