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revision 1.4, Tue Jan 12 20:23:30 2010 UTC revision 1.7, Tue Jan 19 17:05:06 2010 UTC
# Line 62  Line 62 
62  my $sims_peg_synonyms = "$sims_data_dir/peg.synonyms";  my $sims_peg_synonyms = "$sims_data_dir/peg.synonyms";
63  my $sims_keep_count = 300;  my $sims_keep_count = 300;
64    
65    my $job48 = new Job48($job_dir);
66    my $meta = $job48->meta;
67    
68    my $host = `hostname`;
69    chomp $host;
70    $meta->add_log_entry($0, "Running phases @phase on $host");
71    
72  #  #
73  # Emulate execution of SGE parallel environment via the  # Emulate execution of SGE parallel environment via the
74  # --parallel N argument.  # --parallel N argument.
# Line 72  Line 79 
79      $ENV{NSLOTS} = $parallel;      $ENV{NSLOTS} = $parallel;
80  }  }
81    
82  if ($phase == 1)  if ($phase{1})
83  {  {
84      &do_upload($job);      &do_upload($job);
85      &do_rp($job);      &do_rp($job);
86  }  }
87    
88  if ($phase == 2)  if ($phase{2})
89  {  {
90      &do_qc($job);      &do_qc($job);
91      &do_correction($job);      &do_correction($job);
92      &do_sims_preprocess($job);      &do_sims_preprocess($job);
93  }  }
94    
95  if ($phase == 3)  if ($phase{3})
96  {  {
97      #      #
98      # If running inside a SGE task array job, execute      # If running inside a SGE task array job, execute
# Line 101  Line 108 
108      }      }
109  }  }
110    
111  if ($phase == 4)  if ($phase{4})
112  {  {
113      &run("$FIG_Config::bin/rp_postproc_sims", $job->dir, $sims_nr_len, $sims_peg_synonyms, $sims_keep_count);      &do_sims_postprocess($job);
114      &do_bbhs($job);      &do_bbhs($job);
115      &do_auto_assign($job);      &do_auto_assign($job);
116      &do_glue_contigs($job);      &do_glue_contigs($job);
# Line 197  Line 204 
204          die "Tasks not found";          die "Tasks not found";
205      }      }
206    
207        for my $task ($task_start .. $task_end)
208        {
209            $ENV{SGE_TASK_ID} = $task;
210            &run("$FIG_Config::bin/rp_compute_sims", $job->dir);
211        }
212    }
213    
214    sub do_sims_postprocess
215    {
216        my($job) = @_;
217    
218      my $sims_nr_len = $sims_nr;      my $sims_nr_len = $sims_nr;
219      if (-f "$sims_nr-len.btree")      if (-f "$sims_nr-len.btree")
220      {      {
221          $sims_nr_len = "$sims_nr-len.btree";          $sims_nr_len = "$sims_nr-len.btree";
222      }      }
223    
224      for my $task ($task_start .. $task_end)      &run("$FIG_Config::bin/rp_postproc_sims", $job->dir, $sims_nr_len, $sims_peg_synonyms, $sims_keep_count);
     {  
         $ENV{SGE_TASK_ID} = $task;  
         &run("$FIG_Config::bin/rp_compute_sims", $job->dir);  
     }  
225  }  }
226    
227  sub do_bbhs  sub do_bbhs

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