view release on metacpan or  search on metacpan

lib/Alien/SeqAlignment/last.pm  view on Meta::CPAN

  use strict;
  use warnings;
  package Alien::SeqAlignment::last;
$Alien::SeqAlignment::last::VERSION = '0.02';
use parent qw( Alien::Base );
=head1 NAME

Alien::SeqAlignment::edlib - find, build and install the last tools

=head1 VERSION

version 0.02

=head1 SYNOPSIS

To execute the last set of tools, you can use the following code:

 use Alien::SeqAlignment::last;
 use Env qw( @PATH );
 unshift @PATH, Alien::SeqAlignment::last->bin_dir;

Now you can run the last tools as:

 system Alien::SeqAlignment::last->lastal (options);    
 system Alien::SeqAlignment::last->lastdb (options); 
 system Alien::SeqAlignment::last->maf_convert (options); 
 system Alien::SeqAlignment::last->train (options); 
 system Alien::SeqAlignment::last->split_or_splice (options); 
 system Alien::SeqAlignment::last->split_or_splice_pe (options); 
 system Alien::SeqAlignment::last->pe_probs (options);

=head1 DESCRIPTION

This distribution provides last so that it can be used by other
Perl distributions that are on CPAN.  The source code will be downloaded
from the last Gitlab repo, and if that fails it will use the location of a
fork by the author of this Perl module. The build provides the various  
CLI tools in the last and last-pair-pe suites. 
Parallelization requires the installation of the GNU parallel package.
If this is not available, the installation will terminate. In that case,
install GNU Parallel from https://www.gnu.org/software/parallel/ and 
re-attempt installation of this Alien.

=cut

=head1 METHODS

=head2 lastal

 Alien::SeqAlignment::last->lastal

Returns the command name for running the CLI version of the last aligner.
The latter finds local alignments between query sequences, and
reference sequences that have been collected into a database using lastdb.

=cut

sub lastal {
    my ($class) = @_;
  $class->runtime_prop->{command}->{lastal} ;
}

=head2 dbbuild

 Alien::SeqAlignment::last->dbbuild