Build.PL

   1 #!/usr/bin/perl
   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 {
  25     eval { require XML::SAX; 1; };
  26
  27     unless ($@) {
  28         if ( grep { $_->{Name} =~ 'XML::SAX::RTF' } @{ XML::SAX->parsers() } )
  29         {
  30             warn <<WARN;
  31
  32 ############################# WARNING #############################
  33
  34 XML::SAX::RTF is not XML::SAX-compliant but is registered as an
  35 XML::SAX parser.  If used as the primary parser, modules requiring
  36 XML::SAX will NOT work. Please install another XML::SAX-compliant
  37 module and modify your local ParserDetails.ini file per XML::SAX
  38 docs to remove references to XML::SAX::RTF.
  39
  40 ############################# WARNING #############################
  41
  42 WARN
  43             sleep 2;
  44         }
  45     }
  46 }
  47
  48 my %recommends = (
  49
  50     # AcePerl support is deprecated, per LDS - cjfields - 5-5-2011
  51
  52     #'Ace'                       => [0,
  53     #    'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'],
  54
  55     'Algorithm::Munkres' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ],
  56
  57     'Array::Compare' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ],
  58
  59     # this won't actually install due to circular dep, but we have no way of
  60     # doing a post-install the [circular dependency!] specifies it is only
  61     # installed on explicit request for this specific module, not when simply
  62     # choosing to install 'all' modules
  63
  64     #'Bio::ASN1::EntrezGene'     => [0,
  65     #    'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'],
  66
  67     'Bio::Phylo' => [
  68         0,
  69         'NeXML related modules/Bio::AlignIO::nexml,Bio::Nexml::Factory,'
  70             . 'Bio::SeqIO::nexml,Bio::TreeIO::nexml'
  71     ],
  72
  73     'Clone' => [ 0, 'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3' ],
  74
  75     'Convert::Binary::C' =>
  76         [ 0, 'Strider functionality/Bio::SeqIO::strider' ],
  77
  78     'DB_File' => [ 0, 'Database functionality/Bio::Assemby,Bio::DB' ],
  79
  80     'Error' => [
  81         0, 'OO-based exception handling (very optional)/Bio::Root::Exception'
  82     ],
  83
  84     'HTML::TableExtract' => [
  85         0, 'HTML parsing/Bio::DB::SeqVersion::gi'
  86     ],
  87
  88     'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ],
  89
  90     'Graph' => [
  91         0.50,
  92         'Phylogenetic Networks, ontology engine implementation, contig analysis'
  93             . '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'
  94             . 'Bio::Assembly::Tools::ContigSpectrum'
  95     ],
  96
  97     'GraphViz' => [
  98         0, 'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz'
  99     ],
 100
 101     'HTML::Entities' =>
 102         [ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ],
 103
 104     'HTML::HeadParser' => [
 105         3,
 106         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'
 107     ],
 108
 109     'HTML::TableExtract' =>
 110         [ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ],
 111
 112     'HTTP::Request::Common' => [
 113         0,
 114         'GenBank+GenPept sequence retrieval, remote http Blast jobs'
 115             . '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'
 116             . 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'
 117     ],
 118
 119     'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ],
 120
 121     'IO::Scalar' => [
 122         0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'
 123     ],
 124
 125     'List::MoreUtils' => [
 126         0,
 127         'Back- or reverse-translation of sequences/'
 128             . 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'
 129     ],
 130
 131     'LWP::UserAgent' => [
 132         0,
 133         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'
 134     ],
 135
 136     'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ],
 137
 138     'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],
 139
 140     'SOAP::Lite' => [ 0, 'Bibliographic queries/Bio::DB::Biblio::soap' ],
 141
 142     'Sort::Naturally' => [
 143         0,
 144         'Sort lexically, but sort numeral parts numerically/'
 145             . 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'
 146     ],
 147
 148     'Spreadsheet::ParseExcel' =>
 149         [ 0, 'Parsing Excel files/Bio::SeqIO::excel' ],
 150
 151     'Storable' => [
 152         2.05,
 153         'Storing sequence objects in local file cache/'
 154             . 'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'
 155             . 'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'
 156     ],
 157
 158     'SVG' => [ 2.26, 'Creating SVG images/Bio::Draw::Pictogram' ],
 159
 160     'SVG::Graph' => [ 0.01, 'Creating SVG images/Bio::TreeIO::svggraph' ],
 161
 162     'Text::ParseWords' =>
 163         [ 0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader' ],
 164
 165     'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ],
 166
 167     'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ],
 168
 169     'XML::LibXML' =>
 170         [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ],
 171
 172     'XML::Parser' => [ 0, 'Parsing XML/Bio::Biblio::IO::medlinexml' ],
 173
 174     'XML::Parser::PerlSAX' => [
 175         0,
 176         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 177         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'
 178     ],
 179
 180     'XML::SAX' => [
 181         0.15,
 182         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'
 183     ],
 184
 185     'XML::SAX::Writer' => [ 0, 'Writing XML/Bio::SeqIO::tigrxml' ],
 186
 187     'XML::Simple' => [
 188         0,
 189         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'
 190     ],
 191
 192     'XML::Twig' => [
 193         0,
 194         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'
 195             . 'Bio::DB::Biblio::eutils'
 196     ],
 197
 198     'XML::Writer' => [
 199         0.4,
 200         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'
 201             . 'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'
 202             . 'Bio::SearchIO::Writer::BSMLResultWriter'
 203     ],
 204
 205     'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ],
 206 );
 207
 208 my $mysql_ok = 0;
 209
 210 my @drivers = available_drivers();
 211
 212 # Set up the Bio::Root::Build object
 213 my $build = Bio::Root::Build->new(
 214     module_name   => 'Bio',
 215     dist_name     => 'BioPerl',
 216     dist_version  => '1.006925',
 217     dist_author   => 'BioPerl Team <bioperl-l@bioperl.org>',
 218     dist_abstract => 'Bioinformatics Toolkit',
 219     license       => 'perl',
 220     requires      => {
 221         'perl'       => '5.6.1',
 222         'IO::String' => 0,               # why is this required?
 223         'Data::Stag' => 0.11,            # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 224         'Scalar::Util' => 0,             # not in Perl 5.6.1, arrived in core in 5.7.3
 225         'ExtUtils::Manifest' => '1.52',  # allows spaces in file names
 226     },
 227
 228     build_requires => {
 229         'CPAN'          => 1.81,
 230         'Module::Build' => 0.2805,
 231         'Test::Harness' => 2.62,
 232         'Test::Most'    => 0,
 233         'URI::Escape'   => 0
 234     },
 235
 236     recommends => {
 237         # reverted to a simple Module::Build-compatible hash, but we keep
 238         # additional data in the %recommends hash above. May be converted to
 239         # something simpler if there aren't complaints down the line.
 240         map { $_ => $recommends{$_}[0] } sort keys %recommends
 241     },
 242
 243     get_options => {
 244         accept => {},
 245         network => {} # say 'perl Build.PL --network' to manually request network tests
 246     },
 247
 248     auto_features => {
 249         'EntrezGene' => {
 250             description => "Presence of Bio::ASN1::EntrezGene",
 251             requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 252         },
 253
 254         'DB_File Tests' => {
 255             description => "BDB tests for Bio::DB::SeqFeature::Store",
 256             requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 257         },
 258
 259         'Bio::DB::GFF Tests' => {
 260             description =>
 261                 "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 262             requires => { 'DBI' => 0 },
 263         },
 264
 265         'MySQL Tests' => {
 266             description =>
 267                 "MySQL-related tests for Bio::DB::SeqFeature::Store",
 268             requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
 269         },
 270
 271         'Pg Tests' => {
 272             description =>
 273                 "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 274             requires => { 'DBI' => 0, 'DBD::Pg' => 0 },
 275         },
 276
 277         'SQLite Tests' => {
 278             description =>
 279                 "SQLite-related tests for Bio::DB::SeqFeature::Store",
 280             requires => { 'DBI' => 0, 'DBD::SQLite' => 0 },
 281         },
 282
 283         'Network Tests' => {
 284             description => "Enable tests that need an internet connection",
 285             requires    => { 'LWP::UserAgent' => 0 },
 286         }
 287     },
 288     dynamic_config       => 1,
 289     recursive_test_files => 1,
 290
 291     # Extra files needed for BioPerl modules
 292     xml_files => {
 293         './Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'
 294     },
 295
 296 #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 297 #script_files       => [] # scripts in scripts directory are installed on-demand
 298 );
 299
 300 my $accept = $build->args('accept');
 301
 302 my $proceed = prompt_for_biodb($accept)
 303     if $build->feature('Bio::DB::GFF')
 304     || $build->feature('MySQL Tests')
 305     || $build->feature('Pg Tests')
 306     || $build->feature('SQLite Tests');
 307
 308 # Handle auto features
 309 if ( $proceed && $build->feature('DB_File Tests') ) {
 310
 311     # will return without doing anything if user chose not to run tests during
 312     make_bdb_test();
 313 }
 314 if ($proceed
 315     && (   $build->feature('MySQL Tests')
 316         || $build->feature('Pg Tests')
 317         || $build->feature('SQLite Tests') )
 318     ) {
 319     make_dbi_test();
 320 }
 321
 322 # Ask questions
 323 $build->choose_scripts($accept);
 324
 325 if ( $build->args('network') ) {
 326     if ( $build->feature('Network Tests') ) {
 327         $build->notes( network => 1 );
 328         $build->log_info("  - will run internet-requiring tests\n");
 329     } else {
 330         $build->notes( network => 0 );
 331         $build->log_info(
 332             "  - Missing LWP::UserAgent, can't run network tests\n");
 333     }
 334 } else {
 335     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 336 }
 337
 338 # Add additional files here
 339 $build->add_build_element('xml');
 340
 341 # Create the build script and exit
 342 $build->create_build_script;
 343
 344 exit;
 345
 346 ########################## Helper subs ##########################
 347
 348 sub make_bdb_test {
 349     my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 350     my $path  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature_BDB.t' );
 351     unlink($path) if ( -e $path );
 352     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 353     print $F <<END;
 354 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 355 END
 356     close $F;
 357     $build->add_to_cleanup($path);
 358
 359     #$build->add_to_manifest_skip($path);
 360 }
 361
 362 sub available_drivers {
 363     eval { require DBI; 1; }; # if not installed, this sub won't actually be called
 364     return if $@;
 365     @drivers = DBI->available_drivers;
 366     unless ( grep {/mysql|Pg|SQLite/i} @drivers ) {
 367         $mysql_ok = 0;
 368         return
 369             "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 370     }
 371     $mysql_ok = 1;
 372     return @drivers;
 373 }
 374
 375 sub make_dbi_test {
 376     my $dsn = $build->notes('test_dsn') || return;
 377     my $path0  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 378     my $driver = $build->notes('dbd_driver');
 379     my $path   = File::Spec->catfile( 't', 'LocalDB',
 380           ( $driver eq 'mysql' )  ? 'SeqFeature_mysql.t'
 381         : ( $driver eq 'SQLite' ) ? 'SeqFeature_SQLite.t'
 382         :                           'SeqFeature_Pg.t' );
 383     my $test_db = $build->notes('test_db');
 384     my $user    = $build->notes('test_user');
 385     my $pass    = $build->notes('test_pass');
 386     open my $F, '>', $path
 387         or die "Could not write file '$path' for DBI test: $!\n";
 388     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 389     $str .= " -user $user"     if $user;
 390     $str .= " -password $pass" if $pass;
 391     print $F <<END;
 392 system '$^X $str';
 393 END
 394     close $F;
 395     $build->add_to_cleanup($path);
 396     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 397
 398     #$build->add_to_manifest_skip($path);
 399 }
 400
 401 sub test_biodbgff {
 402     eval { require DBI; }; # if not installed, this sub won't actually be called
 403     return if $@;
 404     @drivers = DBI->available_drivers;
 405     unless ( grep {/mysql|Pg|Oracle/i} @drivers ) {
 406         return "MySQL, Pg nor Oracle DBI drivers are installed";
 407     }
 408     return;
 409 }
 410
 411 sub prompt_for_biodb {
 412     my $accept = shift;
 413     my $proceed = $accept ? 0 : $build->y_n(
 414         "Do you want to run the Bio::DB::GFF or "
 415             . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
 416         'n'
 417     );
 418
 419     if ($proceed) {
 420         my @driver_choices;
 421         foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
 422             if ( grep {/$poss/i} @drivers ) {
 423                 my $choice = $poss;
 424                 $choice =~ s/^(.)/[$1]/;
 425                 push( @driver_choices, $choice );
 426             }
 427         }
 428
 429         my $driver;
 430         if ( @driver_choices > 1 ) {
 431             my ($default) = $driver_choices[0] =~ /\[(.)/;
 432             $driver = $build->prompt(
 433                 "Which database driver should be used? "
 434                     . join( " ", @driver_choices ),
 435                 $default
 436             );
 437         } else {
 438             ($driver) = $driver_choices[0] =~ /\[(.)/;
 439         }
 440         if ( $driver =~ /^[mM]/ ) {
 441             $driver = 'mysql';
 442         } elsif ( $driver =~ /^[pP]/ ) {
 443             $driver = 'Pg';
 444         } elsif ( $driver =~ /^[oO]/ ) {
 445             $driver = 'Oracle';
 446         } elsif ( $driver =~ /^[sS]/ ) {
 447             $driver = 'SQLite';
 448         }
 449
 450         my $test_db = $build->prompt(
 451             "Which database should I use for testing the $driver driver?\n"
 452                 . "This database should already be present but doesn't have to "
 453                 . "be preloaded for any schema",
 454             'test'
 455         );
 456         my $test_host = $build->prompt(
 457             "On which host is database '$test_db' running (hostname, ip address or host:port)",
 458             'localhost'
 459         );
 460         my $test_user = $build->prompt(
 461             "User name for connecting to database '$test_db'?", 'undef' );
 462         my $test_pass = $build->prompt(
 463             "Password for connecting to database '$test_db'?", 'undef' );
 464
 465         my $use_host = 1;
 466         if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
 467             $use_host = 0;
 468         }
 469
 470         my $test_dsn;
 471         if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
 472             $test_dsn = "dbi:$driver:dbname=$test_db";
 473             $mysql_ok = 0;
 474         } else {
 475             $test_dsn = "dbi:$driver:database=$test_db";
 476             $mysql_ok = 0;
 477         }
 478         if ($use_host) {
 479             $test_dsn .= ";host=$test_host";
 480         }
 481
 482         $build->notes( dbd_driver => $driver );
 483         $build->notes( test_db    => $test_db );
 484         $build->notes( test_host  => $test_host );
 485         $build->notes(
 486             test_user => $test_user eq 'undef' ? undef : $test_user );
 487         $build->notes(
 488             test_pass => $test_pass eq 'undef' ? undef : $test_pass );
 489         $build->notes( test_dsn => $test_dsn );
 490
 491         $build->log_info(
 492             "  - will run tests with database driver '$driver' and these settings:\n",
 493             "    Database $test_db\n",
 494             "    Host     $test_host\n",
 495             "    DSN      $test_dsn\n",
 496             "    User     $test_user\n",
 497             "    Password $test_pass\n"
 498         );
 499         $build->log_info( "  - will not run the BioDBSeqFeature live "
 500                 . "database tests (requires MySQL or Pg driver)\n" )
 501             unless ( $driver eq 'mysql' or $driver eq 'Pg' );
 502     } else {
 503         $build->log_info(
 504             "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
 505         );
 506     }
 507
 508     $build->log_info("\n");
 509     return $proceed;
 510 }