/usr/share/gmod/chado/bin/config.PLS is in libchado-perl 1.31-4.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 | #!/usr/bin/perl -w
use Config;
use File::Basename qw(&basename &dirname);
use FindBin '$Bin';
use Cwd;
$origdir = cwd;
chdir dirname($0);
$file = basename($0, '.PL','.PLS');
$file = "gmod_$file.pl";
my %OPTIONS;
if (open F,"$Bin/../../build.conf") {
while (<F>) {
next if /^\#/;
chomp;
$OPTIONS{$1} = $2 if /^(\w+)\s*=\s*(.+)/;
}
close F;
}
open OUT,">$file" or die "Can't create $file: $!";
print OUT "$Config{startperl} -w\n";
if ($OPTIONS{LIB}) {
print OUT "use lib '$OPTIONS{LIB}';\n";
}
if ($OPTIONS{PREFIX}) {
print OUT "use lib '$OPTIONS{PREFIX}/lib';\n";
}
print OUT <<'!NO!SUBS!';
use strict;
use Getopt::Long;
=head1 OPTIONS
--database <dbname> Name of the database to use
--available_dbs List of available chado databases
--all_tags List of all parameters known about a database
--has_tag <tag> Returns 1 or 0 on stdout if
the given parameter is available
--get_tag_value <tag> Returns the value for the given tag
--confdir Returns the path for the configuration files
--tmpdir Returns the tmp directory path
--gmod_root Returns the gmod_root path
--user Returns the username for the database
--password Returns the password for the database
--host Returns the host name for the database
--port Returns the port number for the database
--driver Returns the database driver for the database
--name Returns the name of the database
--sqlfile Returns the full path to the DDL file for the database
--organism Returns the common name of the default organism
=cut
GetOptions(
'available_dbs' => \$AVAIL,
'all_tags' => \$ALL_TAGS,
'has_tag=s' => \$HAS_TAG,
'get_tag_value=s' => \$GET_TAG_VALUE,
'confdir' => \$CONFDIR,
'tmpdir' => \$TMPDIR,
'gmod_root:s' => \$GMOD_ROOT,
'user' => \$USER,
'password' => \$PASSWORD,
'host' => \$HOST,
'port' => \$PORT,
'driver' => \$DRIVER,
'name' => \$NAME,
'sqlfile' => \$SQLFILE,
'organism' => \$ORGANISM,
'database:s' => \$DATABASE,
) or ( system ('pod2text', $0), exit -1);
my $gmod_conf = $ENV{'GMOD_ROOT'} || "/var/lib/gmod";
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
chdir $origdir;
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