view release on metacpan or  search on metacpan

lib/Alien/MUSCLE.pm  view on Meta::CPAN

Or using L<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');

=head1 DESCRIPTION

Discover or download and install L<MUSCLE|https://www.drive5.com/muscle/>.

=head1 METHODS

L<Alien::MUSCLE> inherits all the methods from L<Alien::Base> and implements the
following new ones.

=head2 muscle_binary

  # "/installed/path/to/muscle"
  $binary = Alien::MUSCLE->muscle_binary;

lib/Alien/MUSCLE.pm  view on Meta::CPAN

=head2 INFLUENTIAL ENVIRONMENT VARIABLES

Installation may be customised to a limited extent with the following
environment variables:

=over 4

=item ALIEN_MUSCLE_FORCE_BINARY

Setting this variable to a true value will force the download of a pre-built
binary distribution of L<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.

=back

=head1 COPYRIGHT & LICENSE

This library is free software. You can redistribute it and/or modify it under
the same terms as Perl itself.