Build.PL

   1 #!/usr/bin/perl -w
   2
   3 # This is a Module::Build script for Bioperl installation.
   4 # See http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm
   5
   6 # Uses a custom subclass of Module::Build called ModuleBuildBioperl that
   7 # doesn't get installed
   8
   9 # In the future developers may need to alter the requires and recommends and
  10 # possibly Network sections of ModuleBuildBioperl->new() below, but otherwise
  11 # nothing else here is likely to need changing.
  12
  13 use strict;
  14 use ModuleBuildBioperl;
  15
  16 our @drivers;
  17
  18 # Set up the ModuleBuildBioperl object
  19 my $build = ModuleBuildBioperl->new(
  20     module_name         => 'Bio',
  21     dist_name           => 'bioperl',
  22     dist_version_from   => 'Bio/Root/Version.pm',
  23     dist_author         => 'Bioperl Team <bioperl-l@bioperl.org>',
  24     dist_abstract       => 'Bioinformatics Toolkit',
  25     license             => 'artistic',
  26     requires            => {
  27                             'perl'                      => '5.6.1',
  28                             'IO::String'                => 0,
  29                             'DB_File'                   => 0
  30                            },
  31     build_requires      => {
  32                             'Test::More'                => 0,
  33                             'Module::Build'             => 0.2805,
  34                             'Test::Harness'             => 2.62,
  35                             'CPAN'                      => 1.81
  36                            },
  37     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
  38                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
  39                             # this won't actually install due to circular dep, but we have no way of doing a post-install
  40                             'Bio::ASN1::EntrezGene'     => '0/parsing entrezgene/Bio::SeqIO::entrezgene',
  41                             # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
  42                             'Class::AutoClass'          => '1/creating objects/Bio::Graph::SimpleGraph,Bio::Graph::SimpleGraph::Traversal,Bio::Graph::ProteinGraph',
  43                             'Clone'                     => '0/cloning objects/Bio::Graph::ProteinGraph,Bio::Tools::Primer3',
  44                             'Convert::Binary::C'        => '0/strider functionality/Bio::SeqIO::strider',
  45                             'Data::Stag::XMLWriter'     => '0/writing choas xml files/Bio::SeqIO::chaosxml',
  46                             'GD'                        => '1.3/rendering Sequences and Features/Bio::Graphics::Glyph*',
  47                             'GD::SVG'                   => '0/creating SVG images/Bio::Graphics::Panel',
  48                             # we specifically want Graph::Directed, but that has no VERSION
  49                             'Graph'                     => '0/ontology engine implementation for the GO parser/Bio::Ontology::SimpleGOEngine::GraphAdaptor',
  50                             'HTML::Entities'            => '0/remote analysis POST submissions/Bio::SearchIO::blastxml',
  51                             'HTML::Parser'              => '3/screen scraping www.gdb.org/Bio::DB::GDB',
  52                             'HTTP::Request::Common'     => '0/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*',
  53                             'LWP::UserAgent'            => '0/remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::Tools::WebBlat,Bio::WebAgent,Bio::Graphics::Glyph::image',
  54                             'PostScript::TextBlock'     => '0/EPS output/Bio::Tree::Draw::Cladogram',
  55                             'Set::Scalar'               => '0/proper operation/Bio::Tree::Compatible',
  56                             'SOAP::Lite'                => '0/XEMBL Services and Bibliographic queries/Bio::DB::XEMBLService,Bio::DB::Biblio::soap',
  57                             'Spreadsheet::ParseExcel'   => '0/parsing Excel files/Bio::SeqIO::excel',
  58                             'Storable'                  => '0/storing sequence objects in local file cache/Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb',
  59                             'SVG'                       => '2.26/SVG output/Bio::Graphics::Pictogram',
  60                             'SVG::Graph'                => '0.01/creating SVG images/Bio::TreeIO::svggraph',
  61                             'Text::Shellwords'          => '0/test scripts/Bio::Graphics',
  62                             'URI::Escape'               => '0/dealing with web resources/Bio::Tools::WebBlat,Bio::FeatureIO::gff,Bio::FeatureIO::interpro,Bio::DB::Biblio::eutils,Bio::DB::EUtilities::Cookie,Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated',
  63                             'XML::DOM::XPath'           => '0.13/parsing interpro features/Bio::FeatureIO::interpro',
  64                             'XML::Parser'               => '0/parsing xml/Bio::Biblio::IO::medlinexml',
  65                             'XML::Parser::PerlSAX'      => '0/parsing xml/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp',
  66                             'XML::SAX'                  => '0/parsing xml/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
  67                             'XML::SAX::Writer'          => '0/writing xml/Bio::SeqIO::tigrxml',
  68                             # this is just required by XML::Simple, since installation will fail if only XML::SAX::PurePerl is installed
  69                             # should be able to remove this when XML::SAX is bug-fixed for this problem
  70                             # *** to get XML::SAX::ExpatXS to install before XML::Simple, we should recommend a bundle of the two,
  71                             #     instead of recommending them directly... just need to make the bundle...
  72                             'XML::SAX::ExpatXS'         => '0/parsing xml/XML::Simple',
  73                             'XML::Simple'               => '0/parsing xml/Bio::DB::EUtilities',
  74                             'XML::Twig'                 => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils,Bio::Graph::IO::psi_xml',
  75                             'XML::Writer'               => '0.4/parsing and writing xml/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,Bio::SearchIO::Writer::BSMLResultWriter'
  76                            },
  77     get_options         => {
  78                             network => { } # not actually used by anything yet, but in the future say perl Build.PL --network
  79                            },
  80     auto_features       => {
  81                             BioDBSeqFeature_BDB   => {
  82                                                         description      => "BDB tests for Bio::DB::SeqFeature::Store",
  83                                                         feature_requires => { 'DB_File' => 0 } # feature_requires is like requires, execpt that it doesn't trigger installation
  84                                                      },
  85                             BioDBGFF              => {
  86                                                         description      => "BioDBGFF database tests (will need to answer questions before really enabling)",
  87                                                         feature_requires => { 'DBI' => 0 },
  88                                                         excludes_os      => ['mswin'],
  89                                                         test             => \&test_biodbgff # ModuleBuildBioperl unique requirement that after everything else succeeds, supplied code ref must also return undef
  90                                                      },
  91                             BioDBSeqFeature_mysql => {
  92                                                         description      => "MySQL tests for Bio::DB::SeqFeature::Store",
  93                                                         feature_requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
  94                                                         test             => \&test_db
  95                                                      },
  96 # The following code works, but since no tests in the test suite actually make use of this functionality, don't use it yet
  97 #                            Network               => {
  98 #                                                        description => "Enable tests that need an internet connection",
  99 #                                                        requires    => { 'LWP::UserAgent' => 0 },
 100 #                                                        options     => ['network'], # ModuleBuildBioperl unique requirement that --network was supplied
 101 #                                                        test        => \&ModuleBuildBioperl::test_internet
 102 #                                                     }
 103                            },
 104     dynamic_config      => 1,
 105     create_makefile_pl  => 'passthrough'
 106
 107     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 108     #script_files       => [] # scripts in scripts directory are installed on-demand
 109 );
 110
 111 # Handle auto features
 112 if ($build->feature('BioDBSeqFeature_BDB')) {
 113     make_bdb_test();
 114 }
 115 if ($build->feature('BioDBSeqFeature_mysql')) {
 116     make_dbi_test();
 117 }
 118 {
 119     $build->notes(network => $build->feature('Network'));
 120     # then in test script:
 121     #   use Module::Build;
 122     #   my $build = Module::Build->current;
 123     #   my $do_network_tests = $build->notes('network');
 124 }
 125
 126 # Ask questions
 127 $build->choose_scripts;
 128 prompt_for_biodbgff() if $build->feature('BioDBGFF');
 129
 130 # Request that some scripts run post-installation
 131 $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
 132
 133 # Add extra things to MANIFEST.SKIP
 134 $build->add_to_manifest_skip('bioperl.lisp', 'Bio/Tools/WebBlat.pm');
 135
 136 # Create the build script and exit
 137 $build->create_build_script;
 138
 139 exit;
 140
 141
 142 sub make_bdb_test {
 143     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 144     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_BDB.t');
 145     open my $F, ">$path";
 146     print $F <<END;
 147 system 'perl $path0 -adaptor berkeleydb -create 1 -temp 1';
 148 END
 149     close $F;
 150     $build->add_to_cleanup($path);
 151     $build->add_to_manifest_skip($path);
 152 }
 153
 154 sub test_db {
 155     eval {require DBI;};  # if not installed, this sub won't actually be called
 156     unless (eval {DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})}) {
 157         return "Could not connect to test database";
 158     }
 159     return;
 160 }
 161
 162 sub make_dbi_test {
 163     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 164     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_mysql.t');
 165     open my $F,">$path";
 166     print $F <<END;
 167 system 'perl $path0 -adaptor DBI::mysql -create 1 -temp 1 -dsn test';
 168 END
 169     close $F;
 170     $build->add_to_cleanup($path);
 171     $build->add_to_manifest_skip($path);
 172 }
 173
 174 sub test_biodbgff {
 175     eval {require DBI;};  # if not installed, this sub won't actually be called
 176     @drivers = DBI->available_drivers;
 177     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 178         return "MySQL, Pg nor Oracle DBI drivers are installed";
 179     }
 180     return;
 181 }
 182
 183 sub prompt_for_biodbgff {
 184     my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
 185
 186     if ($proceed) {
 187         my @driver_choices;
 188         foreach my $poss ('mysql', 'Pg', 'Oracle') {
 189             if (grep {/$poss/i} @drivers) {
 190                 my $choice = $poss;
 191                 $choice =~ s/^(.)/[$1]/;
 192                 push(@driver_choices, $choice);
 193             }
 194         }
 195
 196         my $driver;
 197         if (@driver_choices > 1) {
 198             my ($default) = $driver_choices[0] =~ /\[(.)/;
 199             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 200         }
 201         else {
 202             ($driver) = $driver_choices[0] =~ /\[(.)/;
 203         }
 204         if ($driver =~ /^[mM]/) {
 205             $driver = 'mysql';
 206         }
 207         elsif ($driver =~ /^[pP]/) {
 208             $driver = 'Pg';
 209         }
 210         elsif ($driver =~ /^[oO]/) {
 211             $driver = 'Oracle';
 212         }
 213
 214         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?", 'test');
 215         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 216         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 217         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 218
 219         my $use_host = 1;
 220         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 221             $use_host = 0;
 222         }
 223
 224         my $test_dsn;
 225         if ($driver eq 'Pg') {
 226             $test_dsn = "dbi:$driver:dbname=$test_db";
 227         }
 228         else {
 229             $test_dsn = "dbi:$driver:database=$test_db";
 230         }
 231         if ($use_host) {
 232             $test_dsn .= ";host=$test_host";
 233         }
 234
 235         $build->notes(dbd_driver => $driver);
 236         $build->notes(test_db => $test_db);
 237         $build->notes(test_host => $test_host);
 238         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 239         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 240         $build->notes(test_dsn => $test_dsn);
 241
 242         $build->log_info("  - will run the BioDBGFF tests with database driver '$driver' and these settings:\n",
 243                         "    Database $test_db\n",
 244                         "    Host     $test_host\n",
 245                         "    DSN      $test_dsn\n",
 246                         "    User     $test_user\n",
 247                         "    Password $test_pass\n");
 248     }
 249     else {
 250         $build->log_info("  - will not run the BioDBGFF live database tests\n");
 251     }
 252
 253     $build->log_info("\n");
 254 }