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Add validation primer code to MACS source
author
Tim Reddy Tim
<treddy@hudsonalpha.org>
Mon, 24 Nov 2008 23:29:53 +0000
(23:29 +0000)
committer
Tim Reddy Tim
<treddy@hudsonalpha.org>
Mon, 24 Nov 2008 23:29:53 +0000
(23:29 +0000)
htswanalysis/scripts/ConfigureTasks.pm
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diff --git
a/htswanalysis/scripts/ConfigureTasks.pm
b/htswanalysis/scripts/ConfigureTasks.pm
index 3aab29c0380bba6415dea5fa3dea1df258edd873..9cf527ae6f678884cab828939a6793d7c5ce46ff 100755
(executable)
--- 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";