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

  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.

METHODS

Alien::MUSCLE inherits all the methods from Alien::Base 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 is straight forward.

If you have 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. 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 - <kiwiroy@cpan.org>