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revision 1.4, Tue Jan 12 20:23:30 2010 UTC revision 1.6, Tue Jan 12 20:29:47 2010 UTC
# Line 72  Line 72 
72      $ENV{NSLOTS} = $parallel;      $ENV{NSLOTS} = $parallel;
73  }  }
74    
75  if ($phase == 1)  if ($phase{1})
76  {  {
77      &do_upload($job);      &do_upload($job);
78      &do_rp($job);      &do_rp($job);
79  }  }
80    
81  if ($phase == 2)  if ($phase{2})
82  {  {
83      &do_qc($job);      &do_qc($job);
84      &do_correction($job);      &do_correction($job);
85      &do_sims_preprocess($job);      &do_sims_preprocess($job);
86  }  }
87    
88  if ($phase == 3)  if ($phase{3})
89  {  {
90      #      #
91      # If running inside a SGE task array job, execute      # If running inside a SGE task array job, execute
# Line 101  Line 101 
101      }      }
102  }  }
103    
104  if ($phase == 4)  if ($phase{4})
105  {  {
106      &run("$FIG_Config::bin/rp_postproc_sims", $job->dir, $sims_nr_len, $sims_peg_synonyms, $sims_keep_count);      &do_sims_postprocess($job);
107      &do_bbhs($job);      &do_bbhs($job);
108      &do_auto_assign($job);      &do_auto_assign($job);
109      &do_glue_contigs($job);      &do_glue_contigs($job);
# Line 197  Line 197 
197          die "Tasks not found";          die "Tasks not found";
198      }      }
199    
200        for my $task ($task_start .. $task_end)
201        {
202            $ENV{SGE_TASK_ID} = $task;
203            &run("$FIG_Config::bin/rp_compute_sims", $job->dir);
204        }
205    }
206    
207    sub do_sims_postprocess
208    {
209        my($job) = @_;
210    
211      my $sims_nr_len = $sims_nr;      my $sims_nr_len = $sims_nr;
212      if (-f "$sims_nr-len.btree")      if (-f "$sims_nr-len.btree")
213      {      {
214          $sims_nr_len = "$sims_nr-len.btree";          $sims_nr_len = "$sims_nr-len.btree";
215      }      }
216    
217      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);  
     }  
218  }  }
219    
220  sub do_bbhs  sub do_bbhs

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