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1 : olson 1.1 # -*- perl -*-
2 :     #
3 :     # Copyright (c) 2003-2006 University of Chicago and Fellowship
4 :     # for Interpretations of Genomes. All Rights Reserved.
5 :     #
6 :     # This file is part of the SEED Toolkit.
7 :     #
8 :     # The SEED Toolkit is free software. You can redistribute
9 :     # it and/or modify it under the terms of the SEED Toolkit
10 :     # Public License.
11 :     #
12 :     # You should have received a copy of the SEED Toolkit Public License
13 :     # along with this program; if not write to the University of Chicago
14 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15 :     # Genomes at veronika@thefig.info or download a copy from
16 :     # http://www.theseed.org/LICENSE.TXT.
17 :     #
18 :    
19 :     use strict;
20 :     use GenomeMeta;
21 :     use FIG;
22 :     use FIG_Config;
23 :     use strict;
24 :     use File::Basename;
25 :    
26 :     @ARGV == 1 or die "Usage: $0 job-dir\n";
27 :    
28 :     my $jobdir = shift;
29 :    
30 :     -d $jobdir or die "$0: job dir $jobdir does not exist\n";
31 :    
32 :     my $genome = &FIG::file_head("$jobdir/GENOME_ID");
33 :     chomp $genome;
34 :     $genome =~ /^\d+\.\d+/ or die "$0: Cannnot find genome ID for jobdir $jobdir\n";
35 :    
36 :     my $meta_file = "$jobdir/meta.xml";
37 :     my $meta = new GenomeMeta($genome, $meta_file);
38 :    
39 :     my $newD = "$jobdir/rp/$genome";
40 :    
41 :     -d $newD or &fatal("genome directory $newD not found");
42 :    
43 :     $meta->set_metadata("status.qc", "in_progress");
44 :    
45 : olson 1.2 my $cmd = "$FIG_Config::bin/assess_gene_call_quality --meta=$meta_file $newD > $newD/quality.report 2>&1";
46 :     $meta->add_log_entry($0, $cmd);
47 :     my $rc = system($cmd);
48 : olson 1.1
49 : olson 1.3 $rc == 0 or &fatal("system $cmd failed with rc=$rc");
50 :    
51 : olson 1.1 $meta->set_metadata("status.qc", "complete");
52 : olson 1.2 $meta->set_metadata("qc.running", "no");
53 : olson 1.1
54 :     sub fatal
55 :     {
56 :     my($msg) = @_;
57 :    
58 :     $meta->add_log_entry($0, ['fatal error', $msg]);
59 : olson 1.4 $meta->set_metadata("status.qc", "error");
60 : olson 1.1
61 :     croak "$0: $msg";
62 :     }
63 :    

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