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-3380
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- refs/tags/genome-3383
- refs/tags/genome-3384
- refs/tags/genome-3385
- refs/tags/genome-3386
- refs/tags/genome-3387
- refs/tags/genome-3388
- refs/tags/genome-3389
- 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
- refs/tags/genome-3398
- 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
- refs/tags/genome-3410
- refs/tags/genome-3411
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- refs/tags/genome-3414
- refs/tags/genome-3415
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- refs/tags/genome-3420
- refs/tags/genome-3421
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- refs/tags/genome-3425
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- refs/tags/genome-3465
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- refs/tags/genome-3472
- refs/tags/genome-3473
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- refs/tags/genome-3475
- refs/tags/genome-3476
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- refs/tags/genome-3493
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- refs/tags/genome-3503
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- refs/tags/genome-3505
- refs/tags/genome-3506
- refs/tags/genome-3507
- refs/tags/genome-3508
- refs/tags/genome-3509
- refs/tags/genome-3510
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- refs/tags/genome-3517
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- refs/tags/genome-3520
- refs/tags/genome-3521
- refs/tags/genome-3522
- refs/tags/genome-3523
- refs/tags/genome-3524
- refs/tags/genome-3525
- refs/tags/genome-3526
- refs/tags/genome-3527
- refs/tags/genome-3528
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- refs/tags/genome-3530
- refs/tags/genome-3531
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- refs/tags/genome-3537
- refs/tags/genome-3538
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- refs/tags/genome-3575
- refs/tags/genome-3576
- refs/tags/genome-3577
- refs/tags/genome-3578
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- refs/tags/genome-3601
- refs/tags/genome-3602
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- refs/tags/genome-3657
- refs/tags/genome-3658
- refs/tags/genome-3659
- refs/tags/genome-3660
- refs/tags/genome-3661
- refs/tags/genome-3662
- refs/tags/genome-3663
- refs/tags/genome-3664
- refs/tags/genome-3665
- refs/tags/genome-3666
- refs/tags/genome-3667
- refs/tags/genome-3668
- refs/tags/genome-3669
- refs/tags/genome-3670
- refs/tags/genome-3671
- refs/tags/genome-3672
- refs/tags/genome-3673
- refs/tags/genome-3674
- refs/tags/genome-3675
- refs/tags/genome-3676
- refs/tags/genome-3677
- refs/tags/genome-3678
- refs/tags/genome-3679
- refs/tags/genome-3680
- refs/tags/genome-3681
- refs/tags/genome-3682
- refs/tags/genome-3683
- refs/tags/genome-3684
- refs/tags/genome-3685
- refs/tags/genome-3686
- refs/tags/genome-3687
- refs/tags/genome-3688
- refs/tags/genome-3689
- refs/tags/genome-3690
- refs/tags/genome-3691
- refs/tags/genome-3692
- refs/tags/genome-3693
- refs/tags/genome-3694
- refs/tags/genome-3695
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- refs/tags/genome-3697
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- refs/tags/genome-3701
- refs/tags/genome-3702
- refs/tags/genome-3703
- refs/tags/genome-3704
- refs/tags/genome-3705
- refs/tags/genome-3706
- refs/tags/genome-3707
- refs/tags/genome-3708
- refs/tags/genome-3709
- refs/tags/genome-3710
- refs/tags/genome-3711
- refs/tags/genome-3712
- refs/tags/genome-3713
- refs/tags/genome-3714
- refs/tags/genome-3715
- refs/tags/genome-3716
- refs/tags/genome-3717
- refs/tags/genome-3718
- refs/tags/genome-3719
- refs/tags/genome-3720
- refs/tags/genome-3721
- refs/tags/genome-3722
- refs/tags/genome-3723
- refs/tags/genome-3724
- refs/tags/genome-3725
- refs/tags/genome-3726
- refs/tags/genome-3727
- refs/tags/genome-3728
- refs/tags/genome-3729
- refs/tags/genome-3730
- refs/tags/genome-3731
- refs/tags/genome-3732
- refs/tags/genome-3733
- refs/tags/genome-3734
- refs/tags/genome-3735
- refs/tags/genome-3736
- refs/tags/genome-3737
- refs/tags/genome-3738
- refs/tags/genome-3739
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- refs/tags/genome-3741
- refs/tags/genome-3742
- refs/tags/genome-3743
- refs/tags/genome-3744
- refs/tags/genome-3745
- refs/tags/genome-3746
- refs/tags/genome-3747
- refs/tags/genome-3748
- refs/tags/genome-3749
- refs/tags/genome-3750
- refs/tags/genome-3751
- refs/tags/genome-3752
- refs/tags/genome-3753
- refs/tags/genome-3754
- refs/tags/genome-3755
- refs/tags/genome-3756
- refs/tags/genome-3757
- refs/tags/genome-3758
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- refs/tags/genome-3760
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- refs/tags/genome-3762
- refs/tags/genome-3763
- refs/tags/genome-3764
- refs/tags/genome-3765
- refs/tags/genome-3766
- refs/tags/genome-3767
- refs/tags/genome-3768
- refs/tags/genome-3769
- refs/tags/genome-3770
- refs/tags/genome-3771
- refs/tags/genome-3772
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- refs/tags/genome-3774
- refs/tags/genome-3775
- refs/tags/genome-3776
- refs/tags/genome-3777
- refs/tags/genome-3778
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- refs/tags/genome-3814
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Tip revision: 868d09a8d65b5bc058da26411bef2119bac34409 authored by Thomas Mooney on 03 April 2014, 22:36:49 UTC
Update expected output to match synopsis changes.
Update expected output to match synopsis changes.
Tip revision: 868d09a
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