/usr/lib/debian-med/bin/gmt is in libgenome-perl 0.06-3.
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 | #!/usr/bin/env perl
use strict;
use warnings;
BEGIN {
# This allows the gmt command to self-serve as a tab completer for the bash shell.
# When "gmt" is run by bash as a tab completer, the code below will service the
# tab-completion request and then exit before doing any real work.
# The code is in an eval to prevent problems on systems which do not have Getopt::Complete
# installed. The code is in a BEGIN block to ensure it still runs before anything else.
if ($ENV{COMP_LINE}) {
eval "use Getopt::Complete::Cache class => 'Genome::Model::Tools', above => 1;";
exit if ($@);
}
};
use above 'Genome';
use Genome::Model::Tools;
Genome::Model::Tools->execute_with_shell_params_and_exit();
=pod
=head1 NAME
gmt - bioinformatics tools for genomics
=head1 SYNOPSIS
# get a top-level list
gmt
# see the MuSiC tools
gmt music
# run the MuSiC smg-test tool
gmt music smg-test
=head1 DESCRIPTION
The B<gmt> command gives command-line access to any Genome Model Tools modules
which are installed on the current system.
Each installed tool group is a sub-command.
Just type B<gmt> and press <ENTER> for a the top-level list and drill down.
=head1 DEVELOPMENT
Installing any new Perl module with a name starting with Genome::Model::Tools will add to the tree.
=head1 AUTHORS
This software is developed by the analysis and engineering teams at
The Genome Center at Washington Univiersity in St. Louis, with funding from
the National Human Genome Research Institute.
=head1 LICENSE
This software is copyright Washington University in St. Louis, 2007-2010.
It is released under the Lesser GNU Public License (LGPL) version 3. See the
associated LICENSE file in this distribution.
=head1 BUGS
For defects with any software in the genome namespace,
contact genome-dev ~at~ genome.wustl.edu.
=cut
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