Final installation of methylseq analysis.

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

diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm
index 8fe851ea12611df2f123b8d9cf8d753aea6e927e..d4348c8b25b10273ac9a0141740909de24d384ea 100755 (executable)
--- a/htswanalysis/scripts/ConfigureTasks.pm
+++ b/htswanalysis/scripts/ConfigureTasks.pm
@@ -52,8 +52,7 @@ my $SUMMARIZE_PROJECT="$root_dir/scripts/SummarizeProject2.pm";
 ###
 ### Important: get the xml file form the server.
 ###
-#my $projects_file = getProjectsXML($parm);
-my $projects_file = "/Users/Data/Projects.xml";
+my $projects_file = getProjectsXML($parm);
 
 my $xmldoc = XML::Simple->new();
 
@@ -101,7 +100,7 @@ close(MAKE);
 
 print STDERR "Project makefile compete. Starting to build tasks\n";
 
-#`cd $data_dir/Projects && make -j 4 -f TaskMakefile > make_tasks.log 2> make_tasks.err`;
+`cd $data_dir/Projects && make -j 4 -f TaskMakefile > make_tasks.log 2> make_tasks.err`;
 
 sub writeProject {
   my $project = shift;
@@ -187,7 +186,7 @@ sub WriteMethylseqTasks {
          $seqcheck .= "\tif [ ! -e $root_dir/reference_data/".$genome."_methylseq_regions ]; then $root_dir/scripts/analys_track_main.py updsts $task \"No methylseq regions available for $genome.\"; fi;\n"; 
 
       my $cmd  = "$outfile: $data_dir/Libraries/$msp1.txt $data_dir/Libraries/$hpa2.txt\n";
-         $cmd .= "\t$METHYLSEQDIR/Methylseq_Analysis $data_dir/Libraries/$msp1.txt $data_dir/Libraries/$hpa2.txt $root_dir/reference_data/".$genome."_methylseq_regions > \$@\n";
+         $cmd .= "\t$METHYLSEQDIR/Methylseq_Analysis $data_dir/Libraries/$msp1.txt $data_dir/Libraries/$hpa2.txt $root_dir/reference_data/".$genome."_methylseq_regions $name > \$@\n";
       writeTask($mseq, $root, $outfile, $cmd, $seqcheck);
 
       $tasks .= $task." ";
@@ -381,8 +380,8 @@ sub WritePeakCallingTasks {
        $cmd .= "\n.PRECIOUS: ".$name.'_peaks.xls '.$name.'_peaks.bed '.$name."_peaks.fasta\n\n";
 
         $cmd .= "\n".$name."_peaks.xls: $data_dir/Libraries/$signal.txt $data_dir/Libraries/$bg.txt\n";
-        $cmd .= "\tcat $data_dir/Libraries/$signal.txt | $root_dir/scripts/align_to_bed.pm | grep -v 'contam' | grep -v 'humRibosomal' > $signal.bed\n";
-        $cmd .= "\tcat $data_dir/Libraries/$bg.txt | $root_dir/scripts/align_to_bed.pm  | grep -v 'contam' | grep -v 'humRibosomal' > $bg.bed\n";
+        $cmd .= "\tcat $data_dir/Libraries/$signal.txt | $root_dir/scripts/align_to_bed.pm | grep -v 'splice' | grep -v 'contam' | grep -v 'humRibosomal' > $signal.bed\n";
+        $cmd .= "\tcat $data_dir/Libraries/$bg.txt | $root_dir/scripts/align_to_bed.pm  | grep -v 'splice' | grep -v 'contam' | grep -v 'humRibosomal' > $bg.bed\n";
         $cmd .= "\t$MACS -t $signal.bed -c ./$bg.bed --name=$name --pvalue=1e-10 --mfold=20 > $name.log 2> $name.err\n";
        $cmd .= "\trm -f $signal.bed $bg.bed\n";
        $cmd .= "\trm -f Background.ELAND.pos $name.ELAND.pos $name.R0.*.bar Background.ELAND.sorted $name.ELAND.sorted\n";