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 Bio::Root::Build
   7
   8 # In the future developers may need to alter the requires and recommends
   9 # sections of Bio::Root::Build->new() below, but otherwise nothing else here is
  10 # likely to need changing.
  11
  12 use strict;
  13 use lib '.';
  14 use Bio::Root::Build;
  15
  16 # XML::SAX::RTF doesn't work with BioPerl, at all, nada, zilch.
  17 #
  18 # Since we're running into this now on CPAN Testers, catch it up front and
  19 # deal with it.
  20 #
  21 # See: https://rt.cpan.org/Ticket/Display.html?id=5943
  22 #      https://redmine.open-bio.org/issues/2975
  23
  24 { eval { require XML::SAX; 1; };
  25
  26 unless ($@) {
  27     if (grep {$_->{Name} =~ 'XML::SAX::RTF'} @{XML::SAX->parsers()}) {
  28         warn <<WARN;
  29 ############################# WARNING #############################
  30
  31 XML::SAX::RTF is not XML::SAX-compliant but is registered as an
  32 XML::SAX parser.  If used as the primary parser, modules requiring
  33 XML::SAX will NOT work. Please install another XML::SAX-compliant
  34 module and modify your local ParserDetails.ini file per XML::SAX
  35 docs to remove references to XML::SAX::RTF.
  36
  37 ############################# WARNING #############################
  38 WARN
  39     sleep 2;
  40     }
  41 }
  42
  43 }
  44
  45 my %recommends = (
  46     'Ace'                       => [0,
  47         'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'],
  48
  49     'Algorithm::Munkres'        => [0,
  50         'Phylogenetic Networks/Bio::PhyloNetwork'],
  51
  52     'Array::Compare'            => [0,
  53         'Phylogenetic Networks/Bio::PhyloNetwork'],
  54
  55     'YAML'                      => [0,
  56         'GenBank->GFF3/bp_genbank2gff3.pl'],
  57
  58     # this won't actually install due to circular dep, but we have no way of
  59     # doing a post-install the [circular dependency!] specifies it is only
  60     # installed on explicit request for this specific module, not when simply
  61     # choosing to install 'all' modules
  62
  63     #'Bio::ASN1::EntrezGene'     => [0,
  64     #    'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'],
  65
  66     'Clone'                     => [0,
  67         'Cloning objects/Bio::Tools::Primer3'],
  68
  69     'Convert::Binary::C'        => [0,
  70         'Strider functionality/Bio::SeqIO::strider'],
  71
  72     'Error'                     => [0,
  73         'OO-based exception handling (very optional)/Bio::Root::Exception'],
  74
  75     'Graph'                     => [0,
  76         'Phylogenetic Networks, ontology engine implementation, contig analysis'.
  77         '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'.
  78         'Bio::Assembly::Tools::ContigSpectrum'],
  79
  80     'GraphViz'                  => [0,
  81         'Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz'],
  82
  83     'HTML::Entities'            => [0,
  84         'Remote analysis POST submissions/Bio::SearchIO::blastxml'],
  85
  86     'HTML::HeadParser'          => [3,
  87         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'],
  88
  89     'HTTP::Request::Common'     => [0,
  90         'GenBank+GenPept sequence retrieval, remote http Blast jobs'.
  91         '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'.
  92         'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'],
  93
  94     'List::MoreUtils'           => [0,
  95         'Back- or reverse-translation of sequences/'.
  96         'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'],
  97
  98     'LWP::UserAgent'            => [0,
  99         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'],
 100
 101     'Math::Random'              => [0,
 102         'Random Phylogenetic Networks/Bio::PhyloNetwork::RandomFactory'],
 103
 104     'PostScript::TextBlock'     => [0,
 105         'EPS output/Bio::Tree::Draw::Cladogram'],
 106
 107     'Set::Scalar'               => [0,
 108         'Proper operation/Bio::Tree::Compatible'],
 109
 110     'SOAP::Lite'                => [0,
 111         'Bibliographic queries/Bio::DB::Biblio::soap'],
 112
 113     'Sort::Naturally'           => [0,
 114         'Sort lexically, but sort numeral parts numerically/'.
 115         'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'],
 116
 117     'Spreadsheet::ParseExcel'   => [0,
 118         'Parsing Excel files/Bio::SeqIO::excel'],
 119
 120     'Storable'                  => [2.05,
 121         'Storing sequence objects in local file cache/'.
 122         'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'.
 123         'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb'],
 124
 125     'SVG'                       => [2.26,
 126         'Creating SVG images/Bio::Draw::Pictogram'],
 127
 128     'SVG::Graph'                => [0.01,
 129         'Creating SVG images/Bio::TreeIO::svggraph'],
 130
 131     'Text::ParseWords'          => [0,
 132         'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'],
 133
 134     'URI::Escape'               => [0,
 135         'Dealing with web resources/Bio::FeatureIO::gff,Bio::FeatureIO::interpro,'.
 136         'Bio::DB::Biblio::eutils,Bio::DB::EUtilParameters,'.
 137         'Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated'],
 138
 139     'XML::DOM::XPath'           => [0.13,
 140         'parsing interpro features/Bio::FeatureIO::interpro'],
 141
 142     'XML::Parser'               => [0,
 143         'parsing xml/Bio::Biblio::IO::medlinexml'],
 144
 145     'XML::Parser::PerlSAX'      => [0,
 146         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 147         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'],
 148
 149     'XML::SAX'                  => [0.15,
 150         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'],
 151
 152     'XML::SAX::Writer'          => [0,
 153         'Writing XML/Bio::SeqIO::tigrxml'],
 154
 155     'XML::Simple'               => [0,
 156         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'],
 157
 158     'XML::Twig'                 => [0,
 159         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'.
 160         'Bio::DB::Biblio::eutils'],
 161
 162     'XML::Writer'               => [0.4,
 163         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'.
 164         'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'.
 165         'Bio::SearchIO::Writer::BSMLResultWriter'],
 166 );
 167
 168 my $mysql_ok = 0;
 169
 170 my @drivers = available_drivers();
 171
 172 # Set up the Bio::Root::Build object
 173 my $build = Bio::Root::Build->new(
 174     module_name         => 'Bio',
 175     dist_name           => 'BioPerl',
 176     dist_version_from   => 'Bio/Root/Version.pm',
 177     dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
 178     dist_abstract       => 'Bioinformatics Toolkit',
 179     license             => 'perl',
 180     no_index            => {'dir'       => [qw(examples/root/lib)]},
 181     requires            => {
 182                             'perl'                      => '5.6.1',
 183                             'IO::String'                => 0,
 184                             'DB_File'                   => 0,
 185                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 186                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
 187                             'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
 188                            },
 189
 190     build_requires      => {
 191                             'Test::More'                => 0,
 192                             'Module::Build'             => 0.2805,
 193                             'Test::Harness'             => 2.62,
 194                             'CPAN'                      => 1.81
 195                            },
 196
 197     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
 198         map {$_ => $recommends{$_}[0]} sort keys %recommends
 199     },
 200
 201     get_options         => {
 202         accept  => { },
 203         network => { } # say 'perl Build.PL --network' to manually request network tests
 204                            },
 205
 206     auto_features       => {
 207         'EntrezGene'    => {
 208             description => "Presence of Bio::ASN1::EntrezGene",
 209             requires    => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 210         },
 211
 212         'DB_File Tests' => {
 213             description => "BDB tests for Bio::DB::SeqFeature::Store",
 214             requires    => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 215          },
 216
 217         'Bio::DB::GFF Tests' => {
 218             description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 219             requires    => { 'DBI' => 0 },
 220          },
 221
 222         'MySQL Tests'   => {
 223             description => "MySQL-related tests for Bio::DB::SeqFeature::Store",
 224             requires    => { 'DBI' => 0, 'DBD::mysql' => 0 },
 225          },
 226
 227         'Pg Tests'      => {
 228             description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 229             requires    => { 'DBI' => 0, 'DBD::Pg' => 0},
 230          },
 231
 232         'SQLite Tests'  => {
 233             description => "SQLite-related tests for Bio::DB::SeqFeature::Store",
 234             requires    => { 'DBI' => 0, 'DBD::SQLite' => 0},
 235          },
 236
 237         'Network Tests'              => {
 238             description      => "Enable tests that need an internet connection",
 239             requires => { 'LWP::UserAgent' => 0 },
 240         }
 241                            },
 242     dynamic_config      => 1,
 243     create_makefile_pl  => 'passthrough',
 244     recursive_test_files => 1,
 245
 246     # Extra files needed for BioPerl modules
 247     xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'},
 248
 249     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 250     #script_files       => [] # scripts in scripts directory are installed on-demand
 251 );
 252
 253 my $accept = $build->args('accept');
 254
 255 my $proceed = prompt_for_biodb($accept) if $build->feature('Bio::DB::GFF')
 256     || $build->feature('MySQL Tests') || $build->feature('MySQL Tests');
 257
 258 # Handle auto features
 259 if ($proceed && $build->feature('DB_File Tests')) {
 260     # will return without doing anything if user chose not to run tests during
 261     make_bdb_test();
 262 }
 263 if ($proceed && ($build->feature('MySQL Tests') ||
 264                  $build->feature('Pg Tests') ||
 265                  $build->feature('SQLite Tests'))) {
 266     make_dbi_test();
 267 }
 268
 269 # Ask questions
 270 $build->choose_scripts($accept);
 271
 272 if ($build->args('network')) {
 273     if ($build->feature('Network Tests')) {
 274         $build->notes(network => 1);
 275         $build->log_info("  - will run internet-requiring tests\n");
 276     }
 277     else {
 278         $build->notes(network => 0);
 279         $build->log_info("  - will not run network tests since I seem to be missing essential network functionality\n");
 280     }
 281 }
 282 else {
 283     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 284 }
 285
 286 # Request that some scripts run post-installation
 287 #$build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
 288
 289 # Add extra things to MANIFEST.SKIP
 290 #$build->add_to_manifest_skip('bioperl.lisp');
 291
 292 # Add additional files here
 293 $build->add_build_element('xml');
 294
 295 # Create the build script and exit
 296 $build->create_build_script;
 297
 298 exit;
 299
 300 ########################## Helper subs ##########################
 301
 302 sub make_bdb_test {
 303     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 304     my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t');
 305     unlink($path) if (-e $path);
 306     open(my $F, ">", $path) || die "Can't create test file\n";
 307     print $F <<END;
 308 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 309 END
 310     close $F;
 311     $build->add_to_cleanup($path);
 312     #$build->add_to_manifest_skip($path);
 313 }
 314
 315 sub available_drivers {
 316     eval {require DBI; 1;};  # if not installed, this sub won't actually be called
 317     @drivers = DBI->available_drivers;
 318     unless (grep {/mysql|Pg|SQLite/i} @drivers) {
 319         $mysql_ok = 0;
 320         return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 321     }
 322     $mysql_ok = 1;
 323     return @drivers;
 324 }
 325
 326 sub make_dbi_test {
 327     my $dsn = $build->notes('test_dsn') || return;
 328     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 329     my $driver = $build->notes('dbd_driver');
 330     my $path = File::Spec->catfile('t', 'LocalDB',
 331                 ($driver eq 'mysql')   ? 'SeqFeature_mysql.t'  :
 332                 ($driver eq 'SQLite')  ? 'SeqFeature_SQLite.t'  :
 333                 'SeqFeature_Pg.t');
 334     my $test_db = $build->notes('test_db');
 335     my $user = $build->notes('test_user');
 336     my $pass = $build->notes('test_pass');
 337     open my $F,">$path";
 338     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 339     $str .= " -user $user" if $user;
 340     $str .= " -password $pass" if $pass;
 341     print $F <<END;
 342 system '$^X $str';
 343 END
 344     close $F;
 345     $build->add_to_cleanup($path);
 346     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 347     #$build->add_to_manifest_skip($path);
 348 }
 349
 350 sub test_biodbgff {
 351     eval {require DBI;};  # if not installed, this sub won't actually be called
 352     @drivers = DBI->available_drivers;
 353     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 354         return "MySQL, Pg nor Oracle DBI drivers are installed";
 355     }
 356     return;
 357 }
 358
 359 sub prompt_for_biodb {
 360     my $accept = shift;
 361     my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
 362                               "Bio::DB::SeqFeature::Store live database tests? ".
 363                               "y/n", 'n');
 364
 365     if ($proceed) {
 366         my @driver_choices;
 367         foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
 368             if (grep {/$poss/i} @drivers) {
 369                 my $choice = $poss;
 370                 $choice =~ s/^(.)/[$1]/;
 371                 push(@driver_choices, $choice);
 372             }
 373         }
 374
 375         my $driver;
 376         if (@driver_choices > 1) {
 377             my ($default) = $driver_choices[0] =~ /\[(.)/;
 378             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 379         }
 380         else {
 381             ($driver) = $driver_choices[0] =~ /\[(.)/;
 382         }
 383         if ($driver =~ /^[mM]/) {
 384             $driver = 'mysql';
 385         }
 386         elsif ($driver =~ /^[pP]/) {
 387             $driver = 'Pg';
 388         }
 389         elsif ($driver =~ /^[oO]/) {
 390             $driver = 'Oracle';
 391         }
 392         elsif ($driver =~ /^[sS]/) {
 393             $driver = 'SQLite';
 394         }
 395
 396         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
 397                                      "This database should already be present but doesn't have to ".
 398                                      "be preloaded for any schema", 'test');
 399         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 400         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 401         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 402
 403         my $use_host = 1;
 404         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 405             $use_host = 0;
 406         }
 407
 408         my $test_dsn;
 409         if ($driver eq 'Pg' || $driver eq 'SQLite') {
 410             $test_dsn = "dbi:$driver:dbname=$test_db";
 411             $mysql_ok = 0;
 412         }
 413         else {
 414             $test_dsn = "dbi:$driver:database=$test_db";
 415             $mysql_ok = 0;
 416         }
 417         if ($use_host) {
 418             $test_dsn .= ";host=$test_host";
 419         }
 420
 421         $build->notes(dbd_driver => $driver);
 422         $build->notes(test_db => $test_db);
 423         $build->notes(test_host => $test_host);
 424         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 425         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 426         $build->notes(test_dsn => $test_dsn);
 427
 428         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 429                         "    Database $test_db\n",
 430                         "    Host     $test_host\n",
 431                         "    DSN      $test_dsn\n",
 432                         "    User     $test_user\n",
 433                         "    Password $test_pass\n");
 434         $build->log_info("  - will not run the BioDBSeqFeature live ".
 435                          "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
 436     }
 437     else {
 438         $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
 439     }
 440
 441     $build->log_info("\n");
 442     return $proceed;
 443 }