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revision 1.59, Thu Apr 1 14:54:57 2004 UTC revision 1.60, Thu Apr 1 22:07:31 2004 UTC
# Line 74  Line 74 
74          my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;          my @errors = `$FIG_Config::bin/verify_genome_directory $genomeF`;
75          if (@errors == 0)          if (@errors == 0)
76          {          {
77              &run("cp -r $genomeF $FIG_Config::organisms; chmod -R 777 $FIG_Config::organisms/$genome");              &run("cp -r $genomeF $FIG_Config::organisms; chmod -R 2777 $FIG_Config::organisms/$genome");
78              chmod 0777, "$FIG_Config::organisms/$genomeF";              chmod 02777, "$FIG_Config::organisms/$genomeF";
79              &run("index_contigs $genome");              &run("index_contigs $genome");
80              &run("compute_genome_counts $genome");              &run("compute_genome_counts $genome");
81              &run("load_features $genome");              &run("load_features $genome");
# Line 699  Line 699 
699          &verify_dir($1);          &verify_dir($1);
700      }      }
701      mkdir($dir,0777) || die "could not make $dir";      mkdir($dir,0777) || die "could not make $dir";
702      chmod 0777,$dir;      chmod 02777,$dir;
703  }  }
704    
705  =pod  =pod
# Line 2788  Line 2788 
2788              print TMP "$feature_id\n$time_made\n$user\n$annotation", (substr($annotation,-1) eq "\n") ? "" : "\n","//\n";              print TMP "$feature_id\n$time_made\n$user\n$annotation", (substr($annotation,-1) eq "\n") ? "" : "\n","//\n";
2789              my $seek2 = tell TMP;              my $seek2 = tell TMP;
2790              close(TMP);              close(TMP);
2791              chmod 0777, $file;              chmod 02777, $file;
2792              my $ln = $seek2 - $seek1;              my $ln = $seek2 - $seek1;
2793              my $rdbH = $self->db_handle;              my $rdbH = $self->db_handle;
2794              if ($rdbH->SQL("INSERT INTO annotation_seeks ( fid, dateof, who, ma, fileno, seek, len ) VALUES ( \'$feature_id\', $time_made, \'$user\', \'$ma\', $fileno, $seek1, $ln )"))              if ($rdbH->SQL("INSERT INTO annotation_seeks ( fid, dateof, who, ma, fileno, seek, len ) VALUES ( \'$feature_id\', $time_made, \'$user\', \'$ma\', $fileno, $seek1, $ln )"))

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