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revision 1.362, Tue Sep 6 19:58:53 2005 UTC revision 1.363, Thu Sep 8 16:12:22 2005 UTC
# Line 491  Line 491 
491          my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;          my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
492          chomp @tmp;          chomp @tmp;
493          &run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr") if (!$skipnr);          &run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr") if (!$skipnr);
494            &run("formatdb -i $FIG_Config::data/Global/nr -p T") if (!$skipnr);
495          &enqueue_similarities(\@tmp);          &enqueue_similarities(\@tmp);
496      }      }
497      if ((-s "$FIG_Config::organisms/$genome/assigned_functions") ||      if ((-s "$FIG_Config::organisms/$genome/assigned_functions") ||
# Line 2350  Line 2351 
2351      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
2352      my($cmd) = @_;      my($cmd) = @_;
2353    
2354      if ($ENV{VERBOSE}) {      if ($ENV{FIG_VERBOSE}) {
2355          my @tmp = `date`;          my @tmp = `date`;
2356          chomp @tmp;          chomp @tmp;
2357          print STDERR "$tmp[0]: running $cmd\n";          print STDERR "$tmp[0]: running $cmd\n";
# Line 12141  Line 12142 
12142          if ((@changes == 1) && ($changes[0] =~ /^\S+\t\S+\t(\S+)\t(\S+)/))          if ((@changes == 1) && ($changes[0] =~ /^\S+\t\S+\t(\S+)\t(\S+)/))
12143          {          {
12144              my($new_loc,$conf) = ($1,$2);              my($new_loc,$conf) = ($1,$2);
12145              if (($ENV{'VERBOSE'}) && open(TMP,"<$FIG_Config::temp/proposed$$"))              if (($ENV{FIG_VERBOSE}) && open(TMP,"<$FIG_Config::temp/proposed$$"))
12146              {              {
12147                  while (defined($_ = <TMP>)) { print STDERR $_ }                  while (defined($_ = <TMP>)) { print STDERR $_ }
12148                  close(TMP);                  close(TMP);

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