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

use strict;
use warnings;
package Alien::SeqAlignment::cutadapt;
$Alien::SeqAlignment::cutadapt::VERSION = '0.05';

use parent qw( Alien::Base );

=head1 NAME

Alien::SeqAlignment::cutadapt - Find or install cutadapt

=head1 VERSION

version 0.05

=head1 SYNOPSIS

Command line tool:

 system 'cutadapt' (list of arguments and options);
 system "cutadapt  (list of argumentns and options)"; # less safe
 
or you can even do this to maintain compatibility with the Alien tool API

 system Alien::SeqAlignment::cutadapt->cutadapt (list of arguments and options)

=head1 DESCRIPTION

This distribution provides the python tool cutadapt so that it can be used by 
other Perl distributions that are on CPAN.  It does this by first trying to
detect an existing install of cutadapt on your system.  If found it
will use that.  If it cannot be found, it will use the Python package installer
pipx to download and install cutadapt in an isolated environment for each
user. Note that after installation one ends up with a tool that can be used
from the shell (i.e. no need for Perl), hence uninstalling the Perl module will
not uninstall cutadapt or pipx. If you would like to uninstall cutadapt, then
you should use pipx to uninstall it as in: 

 pipx uninstall cutadapt.

Note that the installation method of pipx varies by operating system. 
MacOS and Windows users should have working installations of homebrew and scoop 
respectively to use this Perl Alien module.

=head1 METHODS

=head2 cutadapt

 Alien::SeqAlignment::cutadapt->cutadapt

Returns the command name for running the CLI version of the cutadapt CLI. 

=cut

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

=head1 SEE ALSO

=over 4

=item * L<cutadapt|https://cutadapt.readthedocs.io/en/stable/index.html>

Cutadapt finds and removes adapter sequences, primers, poly-A tails and