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     'SOAP::Lite' => [ 0, 'Bibliographic queries/Bio::DB::Biblio::soap' ],
 139
 140     'Sort::Naturally' => [
 141         0,
 142         'Sort lexically, but sort numeral parts numerically/'
 143             . 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'
 144     ],
 145
 146     'Spreadsheet::ParseExcel' =>
 147         [ 0, 'Parsing Excel files/Bio::SeqIO::excel' ],
 148
 149     'Storable' => [
 150         2.05,
 151         'Storing sequence objects in local file cache/'
 152             . 'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'
 153             . 'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'
 154     ],
 155
 156     'SVG' => [ 2.26, 'Creating SVG images/Bio::Draw::Pictogram' ],
 157
 158     'SVG::Graph' => [ 0.01, 'Creating SVG images/Bio::TreeIO::svggraph' ],
 159
 160     'Text::ParseWords' =>
 161         [ 0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader' ],
 162
 163     'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ],
 164
 165     'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ],
 166
 167     'XML::LibXML' =>
 168         [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ],
 169
 170     'XML::Parser' => [ 0, 'Parsing XML/Bio::Biblio::IO::medlinexml' ],
 171
 172     'XML::Parser::PerlSAX' => [
 173         0,
 174         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 175         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'
 176     ],
 177
 178     'XML::SAX' => [
 179         0.15,
 180         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'
 181     ],
 182
 183     'XML::SAX::Writer' => [ 0, 'Writing XML/Bio::SeqIO::tigrxml' ],
 184
 185     'XML::Simple' => [
 186         0,
 187         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'
 188     ],
 189
 190     'XML::Twig' => [
 191         0,
 192         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'
 193             . 'Bio::DB::Biblio::eutils'
 194     ],
 195
 196     'XML::Writer' => [
 197         0.4,
 198         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'
 199             . 'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'
 200             . 'Bio::SearchIO::Writer::BSMLResultWriter'
 201     ],
 202
 203     'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ],
 204 );
 205
 206 my $mysql_ok = 0;
 207
 208 my @drivers = available_drivers();
 209
 210 # Set up the Bio::Root::Build object
 211 my $build = Bio::Root::Build->new(
 212     module_name   => 'Bio',
 213     dist_name     => 'BioPerl',
 214     dist_version  => $Bio::Root::Version::VERSION,
 215     dist_author   => 'BioPerl Team <bioperl-l@bioperl.org>',
 216     dist_abstract => 'Bioinformatics Toolkit',
 217     license       => 'perl',
 218     requires      => {
 219         'perl'       => '5.6.1',
 220         'IO::String' => 0,               # why is this required?
 221         'Data::Stag' => 0.11,            # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 222         'Scalar::Util' => 0,             # not in Perl 5.6.1, arrived in core in 5.7.3
 223         'ExtUtils::Manifest' => '1.52',  # allows spaces in file names
 224     },
 225
 226     configure_requires => {
 227         'Module::Build' => 0.42,
 228     },
 229
 230     build_requires => {
 231         'Module::Build' => 0.42,
 232         'CPAN'          => 1.81,
 233         'Test::Harness' => 2.62,
 234         'Test::Most'    => 0,
 235         'URI::Escape'   => 0
 236     },
 237
 238     recommends => {
 239         # reverted to a simple Module::Build-compatible hash, but we keep
 240         # additional data in the %recommends hash above. May be converted to
 241         # something simpler if there aren't complaints down the line.
 242         map { $_ => $recommends{$_}[0] } sort keys %recommends
 243     },
 244
 245     get_options => {
 246         accept => {},
 247         network => {} # say 'perl Build.PL --network' to manually request network tests
 248     },
 249
 250     auto_features => {
 251         'EntrezGene' => {
 252             description => "Presence of Bio::ASN1::EntrezGene",
 253             requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 254         },
 255
 256         'DB_File Tests' => {
 257             description => "BDB tests for Bio::DB::SeqFeature::Store",
 258             requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 259         },
 260
 261         'Bio::DB::GFF Tests' => {
 262             description =>
 263                 "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 264             requires => { 'DBI' => 0 },
 265         },
 266
 267         'MySQL Tests' => {
 268             description =>
 269                 "MySQL-related tests for Bio::DB::SeqFeature::Store",
 270             requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
 271         },
 272
 273         'Pg Tests' => {
 274             description =>
 275                 "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 276             requires => { 'DBI' => 0, 'DBD::Pg' => 0 },
 277         },
 278
 279         'SQLite Tests' => {
 280             description =>
 281                 "SQLite-related tests for Bio::DB::SeqFeature::Store",
 282             requires => { 'DBI' => 0, 'DBD::SQLite' => 0 },
 283         },
 284
 285         'Network Tests' => {
 286             description => "Enable tests that need an internet connection",
 287             requires    => { 'LWP::UserAgent' => 0 },
 288         }
 289     },
 290     dynamic_config       => 1,
 291     recursive_test_files => 1,
 292
 293     # Extra files needed for BioPerl modules
 294     xml_files => {
 295         './Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'
 296     },
 297
 298 #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 299 #script_files       => [] # scripts in scripts directory are installed on-demand
 300 );
 301
 302 my $accept = $build->args('accept');
 303
 304 my $proceed = prompt_for_biodb($accept)
 305     if $build->feature('Bio::DB::GFF')
 306     || $build->feature('MySQL Tests')
 307     || $build->feature('Pg Tests')
 308     || $build->feature('SQLite Tests');
 309
 310 # Handle auto features
 311 if ( $proceed && $build->feature('DB_File Tests') ) {
 312
 313     # will return without doing anything if user chose not to run tests during
 314     make_bdb_test();
 315 }
 316 if ($proceed
 317     && (   $build->feature('MySQL Tests')
 318         || $build->feature('Pg Tests')
 319         || $build->feature('SQLite Tests') )
 320     ) {
 321     make_dbi_test();
 322 }
 323
 324 # Ask questions
 325 $build->choose_scripts($accept);
 326
 327 if ( $build->args('network') ) {
 328     if ( $build->feature('Network Tests') ) {
 329         $build->notes( network => 1 );
 330         $build->log_info("  - will run internet-requiring tests\n");
 331     } else {
 332         $build->notes( network => 0 );
 333         $build->log_info(
 334             "  - Missing LWP::UserAgent, can't run network tests\n");
 335     }
 336 } else {
 337     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 338 }
 339
 340 # Add additional files here
 341 $build->add_build_element('xml');
 342
 343 # Create the build script and exit
 344 $build->create_build_script;
 345
 346 exit;
 347
 348 ########################## Helper subs ##########################
 349
 350 sub make_bdb_test {
 351     my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 352     my $path  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature_BDB.t' );
 353     unlink($path) if ( -e $path );
 354     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 355     print $F <<END;
 356 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 357 END
 358     close $F;
 359     $build->add_to_cleanup($path);
 360
 361     #$build->add_to_manifest_skip($path);
 362 }
 363
 364 sub available_drivers {
 365     eval { require DBI; 1; }; # if not installed, this sub won't actually be called
 366     return if $@;
 367     @drivers = DBI->available_drivers;
 368     unless ( grep {/mysql|Pg|SQLite/i} @drivers ) {
 369         $mysql_ok = 0;
 370         return
 371             "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 372     }
 373     $mysql_ok = 1;
 374     return @drivers;
 375 }
 376
 377 sub make_dbi_test {
 378     my $dsn = $build->notes('test_dsn') || return;
 379     my $path0  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 380     my $driver = $build->notes('dbd_driver');
 381     my $path   = File::Spec->catfile( 't', 'LocalDB',
 382           ( $driver eq 'mysql' )  ? 'SeqFeature_mysql.t'
 383         : ( $driver eq 'SQLite' ) ? 'SeqFeature_SQLite.t'
 384         :                           'SeqFeature_Pg.t' );
 385     my $test_db = $build->notes('test_db');
 386     my $user    = $build->notes('test_user');
 387     my $pass    = $build->notes('test_pass');
 388     open my $F, '>', $path
 389         or die "Could not write file '$path' for DBI test: $!\n";
 390     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 391     $str .= " -user $user"     if $user;
 392     $str .= " -password $pass" if $pass;
 393     print $F <<END;
 394 system '$^X $str';
 395 END
 396     close $F;
 397     $build->add_to_cleanup($path);
 398     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 399
 400     #$build->add_to_manifest_skip($path);
 401 }
 402
 403 sub test_biodbgff {
 404     eval { require DBI; }; # if not installed, this sub won't actually be called
 405     return if $@;
 406     @drivers = DBI->available_drivers;
 407     unless ( grep {/mysql|Pg|Oracle/i} @drivers ) {
 408         return "MySQL, Pg nor Oracle DBI drivers are installed";
 409     }
 410     return;
 411 }
 412
 413 sub prompt_for_biodb {
 414     my $accept = shift;
 415     my $proceed = $accept ? 0 : $build->y_n(
 416         "Do you want to run the Bio::DB::GFF or "
 417             . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
 418         'n'
 419     );
 420
 421     if ($proceed) {
 422         my @driver_choices;
 423         foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
 424             if ( grep {/$poss/i} @drivers ) {
 425                 my $choice = $poss;
 426                 $choice =~ s/^(.)/[$1]/;
 427                 push( @driver_choices, $choice );
 428             }
 429         }
 430
 431         my $driver;
 432         if ( @driver_choices > 1 ) {
 433             my ($default) = $driver_choices[0] =~ /\[(.)/;
 434             $driver = $build->prompt(
 435                 "Which database driver should be used? "
 436                     . join( " ", @driver_choices ),
 437                 $default
 438             );
 439         } else {
 440             ($driver) = $driver_choices[0] =~ /\[(.)/;
 441         }
 442         if ( $driver =~ /^[mM]/ ) {
 443             $driver = 'mysql';
 444         } elsif ( $driver =~ /^[pP]/ ) {
 445             $driver = 'Pg';
 446         } elsif ( $driver =~ /^[oO]/ ) {
 447             $driver = 'Oracle';
 448         } elsif ( $driver =~ /^[sS]/ ) {
 449             $driver = 'SQLite';
 450         }
 451
 452         my $test_db = $build->prompt(
 453             "Which database should I use for testing the $driver driver?\n"
 454                 . "This database should already be present but doesn't have to "
 455                 . "be preloaded for any schema",
 456             'test'
 457         );
 458         my $test_host = $build->prompt(
 459             "On which host is database '$test_db' running (hostname, ip address or host:port)",
 460             'localhost'
 461         );
 462         my $test_user = $build->prompt(
 463             "User name for connecting to database '$test_db'?", 'undef' );
 464         my $test_pass = $build->prompt(
 465             "Password for connecting to database '$test_db'?", 'undef' );
 466
 467         my $use_host = 1;
 468         if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
 469             $use_host = 0;
 470         }
 471
 472         my $test_dsn;
 473         if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
 474             $test_dsn = "dbi:$driver:dbname=$test_db";
 475             $mysql_ok = 0;
 476         } else {
 477             $test_dsn = "dbi:$driver:database=$test_db";
 478             $mysql_ok = 0;
 479         }
 480         if ($use_host) {
 481             $test_dsn .= ";host=$test_host";
 482         }
 483
 484         $build->notes( dbd_driver => $driver );
 485         $build->notes( test_db    => $test_db );
 486         $build->notes( test_host  => $test_host );
 487         $build->notes(
 488             test_user => $test_user eq 'undef' ? undef : $test_user );
 489         $build->notes(
 490             test_pass => $test_pass eq 'undef' ? undef : $test_pass );
 491         $build->notes( test_dsn => $test_dsn );
 492
 493         $build->log_info(
 494             "  - will run tests with database driver '$driver' and these settings:\n",
 495             "    Database $test_db\n",
 496             "    Host     $test_host\n",
 497             "    DSN      $test_dsn\n",
 498             "    User     $test_user\n",
 499             "    Password $test_pass\n"
 500         );
 501         $build->log_info( "  - will not run the BioDBSeqFeature live "
 502                 . "database tests (requires MySQL or Pg driver)\n" )
 503             unless ( $driver eq 'mysql' or $driver eq 'Pg' );
 504     } else {
 505         $build->log_info(
 506             "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
 507         );
 508     }
 509
 510     $build->log_info("\n");
 511     return $proceed;
 512 }