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     'CGI' => [ 0, 'CGI-y things/Bio::DB::Query::HIVQuery' ],
  74
  75     'Clone' => [ 0, 'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3' ],
  76
  77     'Convert::Binary::C' =>
  78         [ 0, 'Strider functionality/Bio::SeqIO::strider' ],
  79
  80     'DB_File' => [ 0, 'Database functionality/Bio::Assemby,Bio::DB' ],
  81
  82     'Error' => [
  83         0, 'OO-based exception handling (very optional)/Bio::Root::Exception'
  84     ],
  85
  86     'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ],
  87
  88     'Graph' => [
  89         0.50,
  90         'Phylogenetic Networks, ontology engine implementation, contig analysis'
  91             . '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'
  92             . 'Bio::Assembly::Tools::ContigSpectrum'
  93     ],
  94
  95     'GraphViz' => [
  96         0, 'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz'
  97     ],
  98
  99     'HTML::Entities' =>
 100         [ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ],
 101
 102     'HTML::HeadParser' => [
 103         3,
 104         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'
 105     ],
 106
 107     'HTML::TableExtract' =>
 108         [ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ],
 109
 110     'HTTP::Request::Common' => [
 111         0,
 112         'GenBank+GenPept sequence retrieval, remote http Blast jobs'
 113             . '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'
 114             . 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'
 115     ],
 116
 117     'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ],
 118
 119     'IO::Scalar' => [
 120         0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'
 121     ],
 122
 123     'List::MoreUtils' => [
 124         0,
 125         'Back- or reverse-translation of sequences/'
 126             . 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'
 127     ],
 128
 129     'LWP::UserAgent' => [
 130         0,
 131         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'
 132     ],
 133
 134     'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ],
 135
 136     'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],
 137
 138     'Sort::Naturally' => [
 139         0,
 140         'Sort lexically, but sort numeral parts numerically/'
 141             . 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'
 142     ],
 143
 144     'Spreadsheet::ParseExcel' =>
 145         [ 0, 'Parsing Excel files/Bio::SeqIO::excel' ],
 146
 147     'Storable' => [
 148         2.05,
 149         'Storing sequence objects in local file cache/'
 150             . 'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'
 151             . 'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'
 152     ],
 153
 154     'SVG' => [ 2.26, 'Creating SVG images/Bio::Draw::Pictogram' ],
 155
 156     'SVG::Graph' => [ 0.01, 'Creating SVG images/Bio::TreeIO::svggraph' ],
 157
 158     'Text::ParseWords' =>
 159         [ 0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader' ],
 160
 161     'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ],
 162
 163     'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ],
 164
 165     'XML::LibXML' =>
 166         [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ],
 167
 168     'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ],
 169
 170     'XML::Parser::PerlSAX' => [
 171         0,
 172         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 173         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'
 174     ],
 175
 176     'XML::SAX' => [
 177         0.15,
 178         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'
 179     ],
 180
 181     'XML::SAX::Writer' => [ 0, 'Writing XML/Bio::SeqIO::tigrxml' ],
 182
 183     'XML::Simple' => [
 184         0,
 185         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'
 186     ],
 187
 188     'XML::Twig' => [
 189         0,
 190         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez'
 191     ],
 192
 193     'XML::Writer' => [
 194         0.4,
 195         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'
 196             . 'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'
 197             . 'Bio::SearchIO::Writer::BSMLResultWriter'
 198     ],
 199
 200     'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ],
 201 );
 202
 203 my $mysql_ok = 0;
 204
 205 my @drivers = available_drivers();
 206
 207 # Set up the Bio::Root::Build object
 208 my $build = Bio::Root::Build->new(
 209     module_name   => 'Bio',
 210     dist_name     => 'BioPerl',
 211     dist_version  => $Bio::Root::Version::VERSION,
 212     dist_author   => 'BioPerl Team <bioperl-l@bioperl.org>',
 213     dist_abstract => 'Bioinformatics Toolkit',
 214     license       => 'perl',
 215     requires      => {
 216         'perl'       => '5.6.1',
 217         'IO::String' => 0,               # why is this required?
 218         'Data::Stag' => 0.11,            # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 219         'Scalar::Util' => 0,             # not in Perl 5.6.1, arrived in core in 5.7.3
 220         'ExtUtils::Manifest' => '1.52',  # allows spaces in file names
 221     },
 222
 223     configure_requires => {
 224         'Module::Build' => 0.42,
 225     },
 226
 227     build_requires => {
 228         'Module::Build' => 0.42,
 229         'CPAN'          => 1.81,
 230         'Test::Harness' => 2.62,
 231         'Test::Most'    => 0,
 232         'URI::Escape'   => 0
 233     },
 234
 235     recommends => {
 236         # reverted to a simple Module::Build-compatible hash, but we keep
 237         # additional data in the %recommends hash above. May be converted to
 238         # something simpler if there aren't complaints down the line.
 239         map { $_ => $recommends{$_}[0] } sort keys %recommends
 240     },
 241
 242     get_options => {
 243         accept => {},
 244         network => {} # say 'perl Build.PL --network' to manually request network tests
 245     },
 246
 247     auto_features => {
 248         'EntrezGene' => {
 249             description => "Presence of Bio::ASN1::EntrezGene",
 250             requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 251         },
 252
 253         'DB_File Tests' => {
 254             description => "BDB tests for Bio::DB::SeqFeature::Store",
 255             requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 256         },
 257
 258         'Bio::DB::GFF Tests' => {
 259             description =>
 260                 "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 261             requires => { 'DBI' => 0 },
 262         },
 263
 264         'MySQL Tests' => {
 265             description =>
 266                 "MySQL-related tests for Bio::DB::SeqFeature::Store",
 267             requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
 268         },
 269
 270         'Pg Tests' => {
 271             description =>
 272                 "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 273             requires => { 'DBI' => 0, 'DBD::Pg' => 0 },
 274         },
 275
 276         'SQLite Tests' => {
 277             description =>
 278                 "SQLite-related tests for Bio::DB::SeqFeature::Store",
 279             requires => { 'DBI' => 0, 'DBD::SQLite' => 0 },
 280         },
 281
 282         'Network Tests' => {
 283             description => "Enable tests that need an internet connection",
 284             requires    => { 'LWP::UserAgent' => 0 },
 285         }
 286     },
 287     dynamic_config       => 1,
 288     recursive_test_files => 1,
 289
 290     # Extra files needed for BioPerl modules
 291     xml_files => {
 292         './Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'
 293     },
 294
 295 #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 296 #script_files       => [] # scripts in scripts directory are installed on-demand
 297 );
 298
 299 my $accept = $build->args('accept');
 300
 301 my $proceed = prompt_for_biodb($accept)
 302     if $build->feature('Bio::DB::GFF')
 303     || $build->feature('MySQL Tests')
 304     || $build->feature('Pg Tests')
 305     || $build->feature('SQLite Tests');
 306
 307 # Handle auto features
 308 if ( $proceed && $build->feature('DB_File Tests') ) {
 309
 310     # will return without doing anything if user chose not to run tests during
 311     make_bdb_test();
 312 }
 313 if ($proceed
 314     && (   $build->feature('MySQL Tests')
 315         || $build->feature('Pg Tests')
 316         || $build->feature('SQLite Tests') )
 317     ) {
 318     make_dbi_test();
 319 }
 320
 321 # Ask questions
 322 $build->choose_scripts($accept);
 323
 324 if ( $build->args('network') ) {
 325     if ( $build->feature('Network Tests') ) {
 326         $build->notes( network => 1 );
 327         $build->log_info("  - will run internet-requiring tests\n");
 328     } else {
 329         $build->notes( network => 0 );
 330         $build->log_info(
 331             "  - Missing LWP::UserAgent, can't run network tests\n");
 332     }
 333 } else {
 334     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 335 }
 336
 337 # Add additional files here
 338 $build->add_build_element('xml');
 339
 340 # Create the build script and exit
 341 $build->create_build_script;
 342
 343 exit;
 344
 345 ########################## Helper subs ##########################
 346
 347 sub make_bdb_test {
 348     my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 349     my $path  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature_BDB.t' );
 350     unlink($path) if ( -e $path );
 351     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 352     print $F <<END;
 353 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 354 END
 355     close $F;
 356     $build->add_to_cleanup($path);
 357
 358     #$build->add_to_manifest_skip($path);
 359 }
 360
 361 sub available_drivers {
 362     eval { require DBI; 1; }; # if not installed, this sub won't actually be called
 363     return if $@;
 364     @drivers = DBI->available_drivers;
 365     unless ( grep {/mysql|Pg|SQLite/i} @drivers ) {
 366         $mysql_ok = 0;
 367         return
 368             "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 369     }
 370     $mysql_ok = 1;
 371     return @drivers;
 372 }
 373
 374 sub make_dbi_test {
 375     my $dsn = $build->notes('test_dsn') || return;
 376     my $path0  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 377     my $driver = $build->notes('dbd_driver');
 378     my $path   = File::Spec->catfile( 't', 'LocalDB',
 379           ( $driver eq 'mysql' )  ? 'SeqFeature_mysql.t'
 380         : ( $driver eq 'SQLite' ) ? 'SeqFeature_SQLite.t'
 381         :                           'SeqFeature_Pg.t' );
 382     my $test_db = $build->notes('test_db');
 383     my $user    = $build->notes('test_user');
 384     my $pass    = $build->notes('test_pass');
 385     open my $F, '>', $path
 386         or die "Could not write file '$path' for DBI test: $!\n";
 387     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 388     $str .= " -user $user"     if $user;
 389     $str .= " -password $pass" if $pass;
 390     print $F <<END;
 391 system '$^X $str';
 392 END
 393     close $F;
 394     $build->add_to_cleanup($path);
 395     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 396
 397     #$build->add_to_manifest_skip($path);
 398 }
 399
 400 sub test_biodbgff {
 401     eval { require DBI; }; # if not installed, this sub won't actually be called
 402     return if $@;
 403     @drivers = DBI->available_drivers;
 404     unless ( grep {/mysql|Pg|Oracle/i} @drivers ) {
 405         return "MySQL, Pg nor Oracle DBI drivers are installed";
 406     }
 407     return;
 408 }
 409
 410 sub prompt_for_biodb {
 411     my $accept = shift;
 412     my $proceed = $accept ? 0 : $build->y_n(
 413         "Do you want to run the Bio::DB::GFF or "
 414             . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
 415         'n'
 416     );
 417
 418     if ($proceed) {
 419         my @driver_choices;
 420         foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
 421             if ( grep {/$poss/i} @drivers ) {
 422                 my $choice = $poss;
 423                 $choice =~ s/^(.)/[$1]/;
 424                 push( @driver_choices, $choice );
 425             }
 426         }
 427
 428         my $driver;
 429         if ( @driver_choices > 1 ) {
 430             my ($default) = $driver_choices[0] =~ /\[(.)/;
 431             $driver = $build->prompt(
 432                 "Which database driver should be used? "
 433                     . join( " ", @driver_choices ),
 434                 $default
 435             );
 436         } else {
 437             ($driver) = $driver_choices[0] =~ /\[(.)/;
 438         }
 439         if ( $driver =~ /^[mM]/ ) {
 440             $driver = 'mysql';
 441         } elsif ( $driver =~ /^[pP]/ ) {
 442             $driver = 'Pg';
 443         } elsif ( $driver =~ /^[oO]/ ) {
 444             $driver = 'Oracle';
 445         } elsif ( $driver =~ /^[sS]/ ) {
 446             $driver = 'SQLite';
 447         }
 448
 449         my $test_db = $build->prompt(
 450             "Which database should I use for testing the $driver driver?\n"
 451                 . "This database should already be present but doesn't have to "
 452                 . "be preloaded for any schema",
 453             'test'
 454         );
 455         my $test_host = $build->prompt(
 456             "On which host is database '$test_db' running (hostname, ip address or host:port)",
 457             'localhost'
 458         );
 459         my $test_user = $build->prompt(
 460             "User name for connecting to database '$test_db'?", 'undef' );
 461         my $test_pass = $build->prompt(
 462             "Password for connecting to database '$test_db'?", 'undef' );
 463
 464         my $use_host = 1;
 465         if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
 466             $use_host = 0;
 467         }
 468
 469         my $test_dsn;
 470         if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
 471             $test_dsn = "dbi:$driver:dbname=$test_db";
 472             $mysql_ok = 0;
 473         } else {
 474             $test_dsn = "dbi:$driver:database=$test_db";
 475             $mysql_ok = 0;
 476         }
 477         if ($use_host) {
 478             $test_dsn .= ";host=$test_host";
 479         }
 480
 481         $build->notes( dbd_driver => $driver );
 482         $build->notes( test_db    => $test_db );
 483         $build->notes( test_host  => $test_host );
 484         $build->notes(
 485             test_user => $test_user eq 'undef' ? undef : $test_user );
 486         $build->notes(
 487             test_pass => $test_pass eq 'undef' ? undef : $test_pass );
 488         $build->notes( test_dsn => $test_dsn );
 489
 490         $build->log_info(
 491             "  - will run tests with database driver '$driver' and these settings:\n",
 492             "    Database $test_db\n",
 493             "    Host     $test_host\n",
 494             "    DSN      $test_dsn\n",
 495             "    User     $test_user\n",
 496             "    Password $test_pass\n"
 497         );
 498         $build->log_info( "  - will not run the BioDBSeqFeature live "
 499                 . "database tests (requires MySQL or Pg driver)\n" )
 500             unless ( $driver eq 'mysql' or $driver eq 'Pg' );
 501     } else {
 502         $build->log_info(
 503             "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
 504         );
 505     }
 506
 507     $build->log_info("\n");
 508     return $proceed;
 509 }