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revision 1.3, Thu Sep 27 19:48:15 2007 UTC revision 1.8, Thu Oct 11 14:38:33 2007 UTC
# Line 5  Line 5 
5  use FIG_Config;  use FIG_Config;
6  use File::Basename;  use File::Basename;
7  use GenomeMeta;  use GenomeMeta;
 #use lib "/home/mkubal/public_html/FIGdisk/dist/releases/dev/FortyEight";  
 #use lib "/home/mkubal/public_html/FIGdisk/dist/releases/dev/PPO";  
8    
9  use DBMaster;  use DBMaster;
10  use Job48;  use Job48;
11  #use SGE;  
12    my $STAGE = "sims";
13    
14  my $fig = new FIG;  my $fig = new FIG;
15    
# Line 41  Line 40 
40  my $fasta = $meta->get_metadata("preprocess.fasta_file");  my $fasta = $meta->get_metadata("preprocess.fasta_file");
41    
42    
43  my $tempf = "/vol/metagenome-48-hour/Data/tblastx-template";  my $tempf;
 #my $tempf = "/home/mkubal/TimeLogic_Templates/tblastx-template";  
44    
45  my @databases = ("nr_2007_0208","16s","lsu","gg");  my @databases = ("nr_2007_0208","16s","lsu","gg","ssu");
46    
47  foreach my $db (@databases){  foreach my $db (@databases){
48    
49        if($db eq "nr_2007_0208"){ $tempf = "/vol/metagenome-48-hour/Data/tblastx-template-nr";}
50        else{$tempf = "/vol/metagenome-48-hour/Data/tblastn-template-others";}
51    
52      my $fa=raelib->read_fasta("$fasta"); # this is a generic method of reading a fasta file into a ref to a hash      my $fa=raelib->read_fasta("$fasta"); # this is a generic method of reading a fasta file into a ref to a hash
53      my @keys=keys %$fa;      my @keys=keys %$fa;
54    
# Line 62  Line 63 
63          map {print OUT ">$_\n",$fa->{$_},"\n"} @subset;          map {print OUT ">$_\n",$fa->{$_},"\n"} @subset;
64          close OUT;          close OUT;
65    
66          my $job = `/decypher/cli/bin/dc_template -query sequences_to_blast -template $tempf -targ $db`;          my $job = `/decypher/cli/bin/dc_template -query sequences_to_blast -template $tempf -targ $db -priority 9`;
67          $job =~ s/^OK1\s+//;          $job =~ s/^OK1\s+//;
68          chomp($job);          chomp($job);
69          push(@jobs,$job);          push(@jobs,$job);
# Line 153  Line 154 
154          }          }
155          close(IN);          close(IN);
156      }      }
157    
158  }  }
159    
160    $job->meta->set_metadata("status.$STAGE", "complete");
161    $job->meta->set_metadata("$STAGE.running", "no");

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