Final installation of methylseq analysis.

[htsworkflow.git] / htswanalysis / scripts / SummarizeProject2.pm

diff --git a/htswanalysis/scripts/SummarizeProject2.pm b/htswanalysis/scripts/SummarizeProject2.pm
index 25ffa0273497b5a05919370da182e92c564c87a3..1ba8334d3d446f3bde32199ec14d5d91c70d65b4 100755 (executable)
--- a/htswanalysis/scripts/SummarizeProject2.pm
+++ b/htswanalysis/scripts/SummarizeProject2.pm
@@ -7,7 +7,7 @@ my $library_info = shift;
 my %libs; 
 my %quest;
 my $expxml = XML::Simple->new();
-my $xml = $expxml->XMLin("Project.xml", ForceArray => [ qw(ComparePeakCalls CompareLibraries PeakCalling ProfileReads qPCR MotifFinding)]);
+my $xml = $expxml->XMLin("Project.xml", ForceArray => [ qw(ComparePeakCalls CompareLibraries PeakCalling ProfileReads qPCR MotifFinding Methylseq)]);
 my @peak_calling = ();
 
 my $project_name = $xml->{Name};
@@ -76,8 +76,10 @@ $qPCR_Summary .= "</TABLE>\n";
 
 my $methylseq_summary = "";
 if(exists($xml->{Methylseq})) {
-  $methylseq_sumary "<TABLE BORDER=1>\n";
+  $methylseq_summary .= "<H2>Methylseq Analysis</H2>\n";
+  $methylseq_summary  .= "<TABLE BORDER=1>\n";
   $methylseq_summary .= "<TR>\n";
+  $methylseq_summary .= "<TD><EM>Task</EM></TD>\n";
   $methylseq_summary .= "<TD><EM>msp1</EM></TD>\n";
   $methylseq_summary .= "<TD><EM>hpa2</EM></TD>\n";
   $methylseq_summary .= "<TD><EM>Assayed</EM></TD>\n";
@@ -93,7 +95,7 @@ if(exists($xml->{Methylseq})) {
     my $msp1   = $xml->{Methylseq}->[$i]->{Msp1}->{Library};
     my $hpa2   = $xml->{Methylseq}->[$i]->{Hpa2}->{Library};
 
-    $methylseq_summary .= `$root_dir/scripts/SummarizeMethylseq.pm $name $task $msp1 $hpa2 $genome`;
+    $methylseq_summary .= `$root_dir/scripts/Summarize_Methylseq.pm $name $task ../../Tasks $msp1 $hpa2 $genome`;
 
   }
   $methylseq_summary .= "</TABLE>\n";
@@ -112,7 +114,7 @@ if(exists($xml->{ProfileReads})) {
     $libs{$lib} = 0;
 
     if($genome eq "scer") { $genome = "sacCer1"; }
-    $profile_summary .= "<TR><TD>$name ($lib)</TD><TD><A HREF=../../Tasks/$task/$lib.wig.gz>$lib.wig.gz</A><BR><A HREF=http://genome.ucsc.edu/cgi-bin/hgTracks?db=$genome&position=chr1:1000-2000&hgt.customText=http://171.65.76.194/Tasks/$task/$lib.wig.gz TARGET=\"_blank\">View in UCSC Genome Browser</A></TD>\n";
+    $profile_summary .= "<TR><TD>$name ($lib)</TD><TD><A HREF=../../Tasks/$task/$lib.wig.gz>$lib.wig.gz</A><BR><A HREF=http://genome.ucsc.edu/cgi-bin/hgTracks?db=$genome&position=chr1:1000-2000&hgt.customText=http://illumina-mac.stanford.edu/Tasks/$task/$lib.wig.gz TARGET=\"_blank\">View in UCSC Genome Browser</A></TD>\n";
     $profile_summary .= "<TD><A HREF=../../Tasks/$task/$lib.profile.gif><IMG WIDTH=300 SRC=../../Tasks/$task/$lib.profile.gif></A></TD></TR>\n";
   }
   $profile_summary .= "</TABLE>\n";
@@ -223,7 +225,7 @@ for(@peak_calling) {
   my $color = "#EEEEFF";
   print "<TR BGCOLOR=$color><TD><B>$hash{Name}</B></TD>";
   print "<TD>$hash{Caller}</TD><TD>$hash{Summary}</TD>\n";
-  print "<TD><A HREF=$hash{outfile}>BED file</A><BR><A HREF=http://genome.ucsc.edu/cgi-bin/hgTracks?db=$hash{Genome}&hgt.customText=http://171.65.76.194/Tasks/$hash{Task}/$hash{outfile}>View in Genome Browser</A></TD><TD><A HREF=$hash{fasta}>FASTA</A></TD>\n";
+  print "<TD><A HREF=$hash{outfile}>BED file</A><BR><A HREF=http://genome.ucsc.edu/cgi-bin/hgTracks?db=$hash{Genome}&hgt.customText=http://illumina-mac.stanford.edu/Tasks/$hash{Task}/$hash{outfile}>View in Genome Browser</A></TD><TD><A HREF=$hash{fasta}>FASTA</A></TD>\n";
   if(exists($hash{primer_design})) { print "<TD><A HREF=$hash{primer_design}>Validation Primers</A></TD>\n"; }
   print "</TR>\n";
 }