https://github.com/genome/genome
- HEAD
- refs/for/master
- refs/heads/chrisamiller-patch-1
- refs/heads/cle
- refs/heads/cle-snapshot
- refs/heads/cle-staging
- refs/heads/cram
- refs/heads/cwltool-path
- refs/heads/gms-pub
- refs/heads/gms-pub-2015.02.22
- refs/heads/gms-pub-2015.03.04
- refs/heads/gms-pub-before-plos-merge-from-master
- refs/heads/gotcloud
- refs/heads/master
- refs/heads/mcallawa_trusty
- refs/heads/model-tests
- refs/heads/model-tests-for-lsf9
- refs/heads/perl-tests
- refs/heads/revert-606-gmt_picard_typos
- refs/heads/snapshot
- refs/tags/AP-103
- refs/tags/genome-3177
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- refs/tags/genome-3387
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- refs/tags/genome-3390
- refs/tags/genome-3391
- refs/tags/genome-3392
- refs/tags/genome-3393
- refs/tags/genome-3394
- refs/tags/genome-3395
- refs/tags/genome-3396
- refs/tags/genome-3397
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- refs/tags/genome-3399
- refs/tags/genome-3400
- refs/tags/genome-3401
- refs/tags/genome-3402
- refs/tags/genome-3403
- refs/tags/genome-3404
- refs/tags/genome-3405
- refs/tags/genome-3406
- refs/tags/genome-3407
- refs/tags/genome-3408
- refs/tags/genome-3409
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- refs/tags/genome-3421
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- refs/tags/genome-3425
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- refs/tags/genome-3507
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- refs/tags/genome-3523
- refs/tags/genome-3524
- refs/tags/genome-3525
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- refs/tags/genome-3527
- refs/tags/genome-3528
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- refs/tags/genome-3664
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- refs/tags/genome-3666
- refs/tags/genome-3667
- refs/tags/genome-3668
- refs/tags/genome-3669
- refs/tags/genome-3670
- refs/tags/genome-3671
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- refs/tags/genome-3673
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- refs/tags/genome-3675
- refs/tags/genome-3676
- refs/tags/genome-3677
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- refs/tags/genome-3752
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- refs/tags/genome-3812
- refs/tags/genome-3813
- refs/tags/genome-3814
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Tip revision: 83d5bd195a34d0c092713bb49531f7aae18b32ac authored by Thomas B. Mooney on 03 April 2018, 21:52:53 UTC
Use Perl's for syntax.
Use Perl's for syntax.
Tip revision: 83d5bd1
genome5.12
#!/usr/bin/env genome-perl5.12
use strict;
use warnings;
BEGIN {
# This allows the genome command to self-serve as a tab completer for the bash shell.
# When "genome" 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 no have Getopt::Complete
# installed. The code is in a BEGIN block to ensure it still runs before anything else.
if ($ENV{COMP_CWORD}) {
eval "use Getopt::Complete::Cache class => 'Genome::Command', above => 1;";
exit if ($@);
}
if ($ENV{COMP_LINE}) {
#for transitioning from older version of completion
#just return no result
exit;
}
};
# do a smart "use lib" for developers
# this only has an effect when your pwd is under Genome/
use above "Genome";
# wrap the base command smartly for the shell
use Genome::Command;
Genome::Command->execute_with_shell_params_and_exit();
=pod
=head1 NAME
genome SUBCOMMAND ...
=head1 SYNOPSIS
genome (list all available commands)
genome project ...
genome taxon ...
genome population-group ...
genome individual ...
genome sample ...
genome instrument-data ...
genome processing-profile ...
genome model ...
genome tools ...
genome disk ...
=head1 DESCRIPTION
This is the top-level tool for working with the genome modeling system and tools.
Just run it with no parameters to get a list of available commands.
Every command and sub-command supports the --help option.
=head1 OPTIONS
These depend on the specific sub-command.
=head1 DEVELOPER NOTE
Running this WITHIN a source tree under the Genome namespace will automatically "use lib" your tree.
=head1 BUGS
Report bugs to software at genome.wustl.edu
=head1 AUTHOR
Eddie Belter
=cut