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revision 1.2, Thu Oct 29 21:21:37 2009 UTC revision 1.3, Mon Jan 4 20:30:23 2010 UTC
# Line 4  Line 4 
4  use Job48;  use Job48;
5  use FIG_Config;  use FIG_Config;
6  use FIG;  use FIG;
7    use Getopt::Long;
8    
9  #  #
10  # Run a jobdirectory in one shot. For batch offload to a remote cluster that  # Run a jobdirectory in one shot. For batch offload to a remote cluster that
# Line 30  Line 31 
31  # export  # export
32  #  #
33    
34    my $parallel = 1;
35    my $phase = 1;
36    
37  @ARGV == 1 or die "Usage: $0 jobdir\n";  my $usage = "Usage: $0 [--parallel N] [--phase N] jobdir\n";
38    
39    if (!GetOptions("parallel=i" => \$parallel,
40                    "phase=i" => \$phase))
41    {
42        die $usage;
43    }
44    
45    @ARGV == 1 or die $usage;
46    
47  my $job_dir = shift;  my $job_dir = shift;
48    
# Line 48  Line 59 
59  my $sims_peg_synonyms = "$sims_data_dir/peg.synonyms";  my $sims_peg_synonyms = "$sims_data_dir/peg.synonyms";
60  my $sims_keep_count = 300;  my $sims_keep_count = 300;
61    
62    if ($parallel > 1)
63    {
64        $ENV{PE} = 'cluster';
65        $ENV{NSLOTS} = $parallel;
66    }
67    
68    if ($phase == 1)
69    {
70  &do_upload($job);  &do_upload($job);
71  &do_rp($job);  &do_rp($job);
72    }
73    
74    if ($phase == 2)
75    {
76  &do_qc($job);  &do_qc($job);
77  &do_correction($job);  &do_correction($job);
78  &do_sims_preprocess($job);  &do_sims_preprocess($job);
79    }
80    
81    if ($phase == 3)
82    {
83  &do_sims($job);  &do_sims($job);
84    }
85    
86    if ($phase == 4)
87    {
88  &do_bbhs($job);  &do_bbhs($job);
89  &do_auto_assign($job);  &do_auto_assign($job);
90  &do_glue_contigs($job);  &do_glue_contigs($job);
91  &do_pchs($job);  &do_pchs($job);
92  &do_scenario($job);  &do_scenario($job);
93  &do_export($job);  &do_export($job);
94    }
95    
96  sub do_upload  sub do_upload
97  {  {
# Line 101  Line 132 
132    
133      my $correction_list = $job->meta->get_metadata("correction.request");      my $correction_list = $job->meta->get_metadata("correction.request");
134    
135        if (ref($correction_list))
136        {
137      my $correction_str = join(",", @$correction_list);      my $correction_str = join(",", @$correction_list);
138      &run("$FIG_Config::bin/rp_correction", $job->dir, $correction_str);      &run("$FIG_Config::bin/rp_correction", $job->dir, $correction_str);
139  }  }
140    }
141    
142  sub do_sims_preprocess  sub do_sims_preprocess
143  {  {

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