#!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;