Build.PL

   1 #!/usr/bin/perl
   2
   3 # This is a Module::Build script for BioPerl-Run installation.
   4 # See http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm
   5
   6 use strict;
   7 use warnings;
   8 use Module::Build;
   9
  10 my $build = Module::Build->subclass(
  11     code => q(
  12
  13         # add dist version to META files
  14         sub get_metadata {
  15             my ($self, %args) = @_;
  16             my $metadata = $self->SUPER::get_metadata(%args);
  17
  18             if (exists $metadata->{provides}) {
  19                 my $ver = $self->dist_version;
  20                 my $pkgs = $metadata->{provides};
  21                 for my $p (keys %{$pkgs}) {
  22                     if (!exists($pkgs->{$p}->{'version'})) {
  23                         $pkgs->{$p}->{'version'} = $ver;
  24                     } else {
  25                         $self->log_warn("Note: Module $p has a set version: ".$pkgs->{$p}->{'version'}."\n")
  26                             if $pkgs->{$p}->{'version'} ne $ver;
  27                     }
  28                 }
  29             }
  30             return $metadata;
  31         }
  32     )
  33     )->new(
  34     dist_name           => 'BioPerl-Run',
  35     dist_version        => '1.007003',
  36     module_name         => 'Bio::Run',
  37     dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
  38     dist_abstract       => 'BioPerl-Run - wrapper toolkit',
  39     license             => 'perl',
  40     config_requires     => {
  41                         'Module::Build' => 0,
  42 },
  43     build_requires      => {
  44                             'Bio::Root::Version' => '1.007000',
  45                             'Bio::Root::Test' => 0,
  46                },
  47     requires            => {
  48                             'perl'               => '5.6.1',
  49                             'Bio::Root::Version' => '1.007000',
  50                             'Bio::Root::Root'    => 0,
  51                            },
  52     recommends          => {
  53                             'Bio::Cluster::SequenceFamily'   => 0, # Bio::Tools::Run::TribeMCL
  54                             'Algorithm::Diff' => 0,     # generating consensus protein family descriptions: Bio::Tools::Run::TribeMCL
  55                             'IPC::Run'        => 0,     # Glimmer and Genemark application wrappers: Bio::Tools::Run::Glimmer Bio::Tools::Run::Genemark
  56                             'IO::String'      => 0,     # generating Bio::Tree::Tree from strings: Bio::Tools::Run::Phylo::Phylip::Consense
  57                             'XML::Twig'       => 0,     # processing XML data: Bio::Tools::Run::EMBOSSacd
  58                             'File::Sort'      => 0,     # BEDTools
  59                             'Config::Any'     => 0,     # MCS, Match
  60                             'Bio::FeatureIO'  => 0,     # MCS, Match, Phastcons
  61                             #'SOAP::Lite'      => 0.716, # A bug that affects SoapEU-unit.t tests was fixed in this version (many levels deep object throws error)
  62                            },
  63     get_options         => {
  64                             accept  => { },
  65                             network => { },
  66                             install_scripts => { }
  67                            },
  68     auto_features       => {
  69                             Network => {
  70                                         description => "Enable tests that need an internet connection",
  71                                         requires    => { 'LWP::UserAgent' => 0 }
  72                                        }
  73                            },
  74     dynamic_config      => 1,
  75     #create_makefile_pl  => 'passthrough'
  76 );
  77
  78 my $accept = $build->args->{accept};
  79
  80 # Optionally have script files installed.
  81 if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
  82     my $files = $build->_find_file_by_type('PLS', 'scripts');
  83
  84     my $script_build = File::Spec->catdir($build->blib, 'script');
  85
  86     my @tobp;
  87     while (my ($file, $dest) = each %$files) {
  88         $dest = 'bp_'.File::Basename::basename($dest);
  89         $dest =~ s/PLS$/pl/;
  90         $dest = File::Spec->catfile($script_build, $dest);
  91         $build->copy_if_modified(from => $file, to => $dest);
  92         push @tobp, $dest;
  93     }
  94
  95     $build->script_files(\@tobp);
  96 }
  97
  98 # Do network tests?
  99 my $do_network_tests = 0;
 100 if ($build->args('network')) {
 101     $do_network_tests = $build->feature('Network');
 102 }
 103 elsif ($build->feature('Network')) {
 104     $do_network_tests = $accept ? 0 : $build->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
 105 }
 106
 107 if ($do_network_tests) {
 108     $build->notes(network => 1);
 109     $build->log_info("  - will run internet-requiring tests\n");
 110     my $use_email = $build->y_n("Do you want to run tests requiring a valid email address? y/n",'n');
 111     if ($use_email) {
 112         my $address = $build->prompt("Enter email address:");
 113         $build->notes(email => $address);
 114     }
 115 }
 116 else {
 117     $build->notes(network => 0);
 118     $build->log_info("  - will not run internet-requiring tests\n");
 119 }
 120
 121 # Create the build script and exit
 122 $build->create_build_script;