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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;

my %application_programs = (
    alimask       => 'alimask',
    hmmalign      => 'hmmalign',
    hmmbuild      => 'hmmbuild',
    hmmconvert    => 'hmmconvert',
    hmmemit       => 'hmmemit',
    hmmfetch      => 'hmmfetch',
    hmmlogo       => 'hmmlogo',
    hmmpgmd       => 'hmmpgmd',
    hmmpgmd_shard => 'hmmpgmd_shard',
    hmmpress      => 'hmmpress',
    hmmsearch     => 'hmmsearch',
    hmmsim        => 'hmmsim',
    hmmstat       => 'hmmstat',
    jackhmmer     => 'jackhmmer',
    makehmmerdb   => 'makehmmerdb',
    nhmmer        => 'nhmmer',
    nhmmscan      => 'nhmmscan',
    phmmer        => 'phmmer',
## Easel minimaps
    esl_afetch     => 'esl-afetch',
    esl_alimanip   => 'esl-alimanip',
    esl_alimap     => 'esl-alimap',
    asl_alimask    => 'esl-alimask',
    esl_alimerge   => 'esl-alimerge',
    esl_alipid     => 'esl-alipid',
    esl_alirev     => 'esl-alirev',
    esl_alistat    => 'esl-alistat',
    esl_compalign  => 'esl-compalign',
    esl_compstruct => 'esl-compstruct',
    esl_construct  => 'esl-construct',
    esl_histplot   => 'esl-histplot',
    esl_mask       => 'esl-mask',
    esl_mixdchlet  => 'esl-mixdchlet',
    esl_reformat   => 'esl-reformat',
    esl_selectn    => 'esl-selectn',
    esl_seqrange   => 'esl-seqrange',
    esl_seqstat    => 'esl-seqstat',
    esl_sfetch     => 'esl-sfetch',
    esl_shuffle    => 'esl-shuffle',
    esl_ssdraw     => 'esl-ssdraw',
    esl_translate  => 'esl-translate',
    esl_weight     => 'esl-weight',
);

probe sub {
    ## see if the nhmmer suite is installed
    my ( $cmd, $stder ) = capture { system( 'nhmmer', '-h' ) };
    my $is_nhmmer_installed_installed = $cmd =~ /HMMER\s+[0-9.]+/m;
    print $is_nhmmer_installed_installed
      ? "The HMMER suite is already installed in your system\n"
      : "The HMMER suite is not installed, so will install from source\n";
    $is_nhmmer_installed_installed ? 'system' : 'share';
};

share {
    start_url 'http://eddylab.org/software/hmmer/hmmer.tar.gz';
    plugin 'Download';
    plugin Extract => 'tar.gz';
    plugin 'Build::Autoconf';
    plugin 'Gather::IsolateDynamic';
    build [
        '%{configure} --prefix=%{.install.prefix}',
        '%{make}',
        '%{make} check',
        '%{make} install',
        'cd easel',
        'make install',
    ];
};

gather sub {
    my ($build) = @_;
    while ( my ( $key, $value ) = each %application_programs ) {
        $build->runtime_prop->{command}->{$key} = $value;
    }
};