#!perl
use Config;
use File::Basename qw(&basename &dirname);
use Cwd;

$origdir = cwd;
chdir dirname($0);
$file = basename($0, '.PL','.PLS');
$file .= $^O eq 'VMS' ? '.com' : '.pl';

open OUT,">$file" or die "Can't create $file: $!";

print "Extracting $file (with variable substitutions)\n";

print OUT <<"!GROK!THIS!";
$Config{startperl}
!GROK!THIS!

# In the following, perl variables are not expanded during extraction.

print OUT <<'!NO!SUBS!';

use strict;
use Bio::GMOD::Query;

$|++;

my $mod  = shift;
my $gene = shift;

$mod && $gene or die "Usage: gmod_query_gene.pl [mod] eg WormBase, FlyBase, SGD) [gene] (e.g. unc-26)";

my $gmod = Bio::GMOD::Query->new(-mod=>$mod);
my $genes = $gmod->fetch(-class=>'gene',-name=>$gene);

print scalar @$genes . " entries found for $gene\n";
foreach (@$genes) {
  print  join("\t",@{$_}),"\n";
}

__END__

=pod

=head1 NAME

gmod_fetch_features.pl - 
gmod_update_installation.pl - Maintain a MOD installation

=head1 USAGE

This script provides a convenient mechanism to maintain a MOD
installation.  It should be excecuted with super user privileges.

  $ gmod_update_installation.pl [options]

=head1 OPTIONS

The following options are generically available for any MOD (default
values in parenthesis):

 MOD:
 --mod       One of WormBase, FlyBase, SGD, etc

 Versions:
 --sync_to   [live || dev] Sync to the current live or development version (live)
 --force     [boolean] Force an update to the live or development version as appropriate (false)
 --version   Update to the provided version (the current live version)

 System paths:
 --tmp       Full path to the temporary directory to hold downloads (/usr/local/gmod/tmp)

 Miscellaneous:
 --purge     [boolean] Purge the tmp download folder following upgrade (false)
 --help      Display this message

Due to the wide variety of installation paths and MOD structures, each
MOD may offer specialized options.  These can be provided as
"--option_name OPTION" which will be passed directly to the
Bio::GMOD::Update::"MOD" object's update() method.  For example, a
typical command to maintain a WormBase installation looks like:

 % gmod_update_installation.pl --analyze_logs --mysql_path /usr/local/mysql/data

For a full description of all available system paths and update
options for your particular MOD, see L<Bio::GMOD::Adaptor> and
L<GMOD::Adaptor::your_mod>.

=head1 Running under cron

You may wish to run this script under cron to ensure that your
installation is always up-to-date.  For my personal installation of
WormBase, I use the following settings:

0 2 * * * /usr/local/bin/gmod_update_installation.pl --sync_to dev

This will check for and install a new version if present at 2 AM in
the morning.

I keep my installation in sync with the development version.  You will
want to use the more stable live version, which you can specify using
"--sync_to live" or by simply leaving off the "--sync_to" option
altogether.

A suggested crontab entry for a simple local installation is:

  gmod_update_intallation.pl --sync_to live --purge 1

A suggested crontab entry for official WormBase mirror sites is:

  gmod_update_intallation.pl --sync_to live --purge 1 --analyze_logs 1

=head1 SEE ALSO

L<Bio::GMOD>, L<Bio::GMOD::Update>

=head1 AUTHOR

Todd Harris <harris@cshl.edu>.

Copyright (c) 2003-2005 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.

=cut


!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
exec("$Config{'eunicefix'} $file") if $Config{'eunicefix'} ne ':';
chdir $origdir;