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use strict;
use warnings;
use alienfile;
use Carp;
use Capture::Tiny qw(capture);
use File::Copy;
use File::Copy::Recursive qw(dircopy);
use HTTP::Tiny;
use Path::Tiny;

configure {
    requires 'Carp';
    requires 'Capture::Tiny';
    requires 'File::Copy';
    requires 'File::Copy::Recursive';
    requires 'HTTP::Tiny';
    requires 'Path::Tiny';
};

die "This Alien does not work on Windows" if $^O eq 'MSWin32';

probe sub {
  
    my ($build) = @_;
    ## see if GNU parallel is installed
    my ( $cmd, $stder ) = capture { system( 'parallel', '--version' ) };
    my $is_gnu_parallel_installed = $cmd =~ /\AGNU\s+parallel\s+[0-9]+/m;
    carp "GNU parallel is not installed\n"
      . "Please install it from https://www.gnu.org/software/parallel/ "
      . "and re-attempt installation of this Alien.\n"
      unless $is_gnu_parallel_installed;

    ## check if all the components of the last suite are installed
    ( $cmd, $stder ) = capture { system( 'lastal', '--version' ) };
    my $is_last_installed = $cmd =~ /\Alastal\s+[0-9]+/m;
    ( $cmd, $stder ) = capture { system( 'last-split', '--version' ) };
    $is_last_installed &&= $cmd =~ /\Alast-split\s+[0-9]+/m;
    ( $cmd, $stder ) = capture { system( 'last-pair-probs', '--version' ) };
    $is_last_installed &&= $cmd =~ /\Alast-pair-probs\s+[0-9]+/m;
    ( $cmd, $stder ) = capture { system( 'maf-convert', '--help' ) };
    $is_last_installed &&= $cmd =~ /\AUsage:/m;
    ( $cmd, $stder ) = capture { system( 'lastdb', '--version' ) };
    $is_last_installed &&= $cmd =~ /lastdb\s+[0-9]+/m;
    ( $cmd, $stder ) = capture { system( 'last-train', '--help' ) };
    $is_last_installed &&= $cmd =~ /\AUsage:/m;
    print $is_last_installed
      ? "The last suite is already installed in your system\n"
      : "The last suite is not installed, so will install from source\n";

    ## check if all the components of the last-split-pe suite are installed
    ( $cmd, $stder ) = capture { system( 'lastal', '--help' ) };
    my $is_last_split_pe_installed = $cmd =~ /\AUsage:/m;
    print $is_last_split_pe_installed
      ? "The last-split-pe suite is already installed in your system\n"
      : "The last-split-pe suite is not installed, so will install from source\n";

    ## set the suite download flags & determine whether to do sys Alien install
    $build->install_prop->{my_to_install_last} = !$is_last_installed;
    $build->install_prop->{my_to_install_last_split_pe} =
      !$is_last_split_pe_installed;
    (        $build->install_prop->{my_to_install_last}
          || $build->install_prop->{my_to_install_last_split_pe} )
      ? 'share'
      : 'system';

};

share {
    download sub {
        my ($build) = @_;
        my $repo_url;
        my $repo_response;

        my $download_dir =
          [ path( $build->install_prop->{root} )->children ]->[0]
          ;    ## create an anonymous reference to get the download directory

   
        ## download last if we have to download it
        if ( $build->install_prop->{my_to_install_last} ) {
            $repo_url =
              'https://gitlab.com/mcfrith/last/-/archive/main/last-main.zip';
            $repo_response = HTTP::Tiny->new->get($repo_url);
            unless ( $repo_response->{success} )
            {    ## failed original download, try my fork
                $repo_url =
'https://gitlab.com/chrisarg1/last/-/archive/main/last-main.zip';
                $repo_response = HTTP::Tiny->new->get($repo_url);
                croak "Failed to download last from either location"
                  unless $repo_response->{success};
            }
            path( $download_dir, 'last-main.zip' )
              ->spew_raw( $repo_response->{content} );
        }

        ##download last_split_pe if we have to download it
        if ( $build->install_prop->{my_to_install_last_split_pe} ) {
            $repo_url =
'https://bitbucket.org/splitpairedend/last-split-pe/get/3f0ce13a347f.zip';
            $repo_response = HTTP::Tiny->new->get($repo_url);
            unless ( $repo_response->{success} )
            {    ## failed original download, try my fork
                $repo_url =
'https://bitbucket.org/chrisarg/last-split-pe/get/3f0ce13a347f.zip';
                $repo_response = HTTP::Tiny->new->get($repo_url);
                croak "Failed to download last_split_pe from either location"
                  unless $repo_response->{success};
            }
            path( $download_dir, 'last-split_pe.zip' )
              ->spew_raw( $repo_response->{content} );
        }
    };

    extract sub {
        my ($build) = @_;
        my ( $extract_dir, $download_dir ) =
          sort( path( $build->install_prop->{root} )->children )