https://github.com/kiwiroy/p5-alien-muscle

Alien module to provide muscle
https://github.com/kiwiroy/p5-alien-muscle

alien bioinformatics perl perl5

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Alien module to provide muscle

• Host: GitHub
• URL: https://github.com/kiwiroy/p5-alien-muscle
• Owner: kiwiroy
• Created: 2020-04-03T08:56:16.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-05-03T22:20:20.000Z (over 4 years ago)
• Last Synced: 2024-10-13T12:01:35.591Z (2 months ago)
• Topics: alien, bioinformatics, perl, perl5
• Language: Perl
• Homepage: https://metacpan.org/pod/Alien::MUSCLE
• Size: 23.4 KB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: Changes

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README

        
# NAME

Alien::MUSCLE - Discover or easy install of MUSCLE

# SYNOPSIS

    use Alien::MUSCLE;

    @cmd = Alien::MUSCLE->muscle_binary;

    push @cmd, (-in => 'sequences.fa', -out => 'results.afa', @opts);

    system { $cmd[0] } @cmd;

Or using [Bio::Tools::Run::Alignment::Muscle](https://metacpan.org/pod/Bio%3A%3ATools%3A%3ARun%3A%3AAlignment%3A%3AMuscle)

    use Env qw(@PATH);

    use Bio::Tools::Run::Alignment::Muscle;

    unshift @PATH, Alien::MUSCLE->bin_dir;

    $muscle = Bio::Tools::Run::Alignment::Muscle->new(@params);

    $align = $muscle->align('sequences.fa');

# DESCRIPTION

Discover or download and install [MUSCLE](https://www.drive5.com/muscle/).

# METHODS

[Alien::MUSCLE](https://metacpan.org/pod/Alien%3A%3AMUSCLE) inherits all the methods from [Alien::Base](https://metacpan.org/pod/Alien%3A%3ABase) and implements the

following new ones.

## muscle\_binary

    # "/installed/path/to/muscle"

    $binary = Alien::MUSCLE->muscle_binary;

The full path to the installed muscle.

## muscle\_dist\_type

    # "source"

    $type = Alien::MUSCLE->muscle_dist_type;

How the program was installed. This is either _source_, if the source

distribution was downloaded and built, or _binary_ if the pre-built software

was downloaded and installed. The pre-built software is statically compiled.

# INSTALLATION

Installing [Alien::MUSCLE](https://metacpan.org/pod/Alien%3A%3AMUSCLE) is straight forward.

If you have [cpanm](https://metacpan.org/pod/cpanm), you only need one line:

    cpanm Alien::MUSCLE

Otherwise, any other cpan client may be used.

## INFLUENTIAL ENVIRONMENT VARIABLES

Installation may be customised to a limited extent with the following

environment variables:

- ALIEN\_MUSCLE\_FORCE\_BINARY

    Setting this variable to a true value will force the download of a pre-built

    binary distribution of [MUSCLE](https://www.drive5.com/muscle/). These versions

    are statically compiled and will not require a compiler on the local machine.

    However there are a limited number of architectures provided and a source

    install may be better in those situations.

# COPYRIGHT & LICENSE

This library is free software. You can redistribute it and/or modify it under

the same terms as Perl itself.

# AUTHORS

Roy Storey -