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  use strict;
  use warnings;
  package Alien::SeqAlignment::bowtie2;
$Alien::SeqAlignment::bowtie2::VERSION = '0.03';
use parent qw( Alien::Base );
=head1 NAME

Alien::SeqAlignment::bowtie2 - find, build and install the bowtie2 tools

=head1 VERSION

version 0.03

=head1 SYNOPSIS

To execute the hmmer3 set of tools, you can use the following code:

 use Alien::SeqAlignment::bowtie2;
 use Env qw( @PATH );
 unshift @PATH, Alien::SeqAlignment::bowtie2->bin_dir;
 
 Alien::SeqAlignment::bowtie2->bowtie2_build      (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_inspect    (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2            (list of arguments)
 
 Alien::SeqAlignment::bowtie2->bowtie2_build_s    (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_inspect_s  (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_align_s    (list of arguments)

 Alien::SeqAlignment::bowtie2->bowtie2_build_l    (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_inspect_l  (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_align_l    (list of arguments)

=head1 DESCRIPTION

This distribution provides bowtie2 so that it can be used by other
Perl distributions that are on CPAN.  The source code will be downloaded
from the github repository and installed in a private location if it is 
not already installed in your system. The bowtie2, bowtie2-build and 
bowtie2-inspect executables are actually wrapper scripts that call binary 
programs as appropriate. The wrappers shield users from having to distinguish 
between "small" (<4GB) and "large" (>4GB)  index formats. 
Also, the bowtie2 (Perl!) wrapper provides some key functionality, 
like the ability to handle compressed inputs, and the functionality 
for --un, --al and related options. While the creators of bowtie2 recommend 
that one always runs the bowtie2 wrappers and not the binaries, application
builders may want to call these functions directly when implementing custom
workflows. Hence, this distributions exposes all functions provided in bowtie2

=head1 METHODS

=head2 bowtie2

 Alien::SeqAlignment::bowtie2->bowtie2            (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_align_s    (list of arguments)
 Alien::SeqAlignment::bowtie2->bowtie2_align_l    (list of arguments)
  
Returns the command name for running the CLI version of the bowtie2 aligner.
The method effectively runs the perl script bowtie2.pl that is distributed
with bowtie2. The methods Alien::SeqAlignment::bowtie2->bowtie2_align_s and
Alien::SeqAlignment::bowtie2->bowtie2_align_l return the binary executables
that align against small and large index formats respectively.


=cut