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revision 1.1, Wed Sep 5 21:41:46 2007 UTC revision 1.3, Tue Sep 25 01:14:57 2007 UTC
# Line 42  Line 42 
42  # Existing SEED data  # Existing SEED data
43  #  #
44    
45  #my $dir_reference_seed_data = "/vol/seed-data-anno-mirror/Data.Jan3";  my $dir_reference_seed_data = "/vol/seed-data-anno-mirror/Data.Jan3";
46  my $dir_reference_seed_data = "/local/FIGdisk/FIG/Data";  #my $dir_reference_seed_data = "/local/FIGdisk/FIG/Data";
47    
48  #  #
49  # RAST server from which to pull genomes to import.  # RAST server from which to pull genomes to import.
# Line 92  Line 92 
92      die "Cannot open previous synonyms file $prev_syn_src: $!\n";      die "Cannot open previous synonyms file $prev_syn_src: $!\n";
93  }  }
94    
95  if (not(-d $prev_sim_dir and <$prev_sim_dir/sims*> > 0))  my @sfiles = <$prev_sim_dir/sims*>;
96    if (not(-d $prev_sim_dir and @sfiles > 0))
97  {  {
98      die "previous sim dir $prev_sim_dir does not appear to contain sims\n";      die "previous sim dir $prev_sim_dir does not appear to contain sims\n";
99  }  }
# Line 164  Line 165 
165  #  #
166  # Scan for RAST jobs to import.  # Scan for RAST jobs to import.
167  #  #
168    # We update our NR component list with the peg features from the job,
169    # and we add the job directory of each to the rast.jobs file. This
170    # will be used later during the installation of these jobs into the SEED.
171    #
172    
173    open(JOBS, ">$jobdir/rast.jobs") or die "Cannot create $jobdir/rast.jobs: $!";
174    
175  my @rast_jobs;  my @rast_jobs;
176  scan_rast_jobs(\@rast_jobs, $dir_rast_jobs);  scan_rast_jobs(\@rast_jobs, $dir_rast_jobs);
177    
178    my @new_rast_jobs;
179  for my $job (@rast_jobs)  for my $job (@rast_jobs)
180  {  {
181      my $gid = $job->genome_id;      my $gid = $job->genome_id;
# Line 178  Line 186 
186    
187      if (exists($NR_dirs{$gid}))      if (exists($NR_dirs{$gid}))
188      {      {
189          die "Rast job $j already exists in SEED server\n";          warn "Rast job $j already exists in SEED server\n";
190            next;
191      }      }
192        push(@new_rast_jobs, $job);
193    
194        print JOBS $job->dir(), "\n";
195    
196      my $fasta = $job->orgdir() . "/Features/peg/fasta";      my $fasta = $job->orgdir() . "/Features/peg/fasta";
197      -f $fasta or die "Job $j has no fasta file in $fasta\n";      -f $fasta or die "Job $j has no fasta file in $fasta\n";
198      $NR_dirs{$gid} = {type => "rast_job", name => $gname, path => $job->orgdir,      $NR_dirs{$gid} = {type => "rast_job", name => $gname, path => $job->orgdir,
199                              fasta_path => $fasta, size => -s _ };                              fasta_path => $fasta, size => -s _ };
200  }  }
201    close(JOBS);
202    @rast_jobs = @new_rast_jobs;
203    
204  open(F, ">$jobdir/all.nr.dirs");  open(F, ">$jobdir/all.nr.dirs");
205  open(F2, ">$jobdir/nr.sources");  open(F2, ">$jobdir/nr.sources");

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