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     'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ],
  85
  86     'Graph' => [
  87         0.50,
  88         'Phylogenetic Networks, ontology engine implementation, contig analysis'
  89             . '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'
  90             . 'Bio::Assembly::Tools::ContigSpectrum'
  91     ],
  92
  93     'GraphViz' => [
  94         0, 'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz'
  95     ],
  96
  97     'HTML::Entities' =>
  98         [ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ],
  99
 100     'HTML::HeadParser' => [
 101         3,
 102         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'
 103     ],
 104
 105     'HTML::TableExtract' =>
 106         [ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ],
 107
 108     'HTTP::Request::Common' => [
 109         0,
 110         'GenBank+GenPept sequence retrieval, remote http Blast jobs'
 111             . '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'
 112             . 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'
 113     ],
 114
 115     'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ],
 116
 117     'IO::Scalar' => [
 118         0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'
 119     ],
 120
 121     'List::MoreUtils' => [
 122         0,
 123         'Back- or reverse-translation of sequences/'
 124             . 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'
 125     ],
 126
 127     'LWP::UserAgent' => [
 128         0,
 129         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'
 130     ],
 131
 132     'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ],
 133
 134     'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],
 135
 136     'SOAP::Lite' => [ 0, 'Bibliographic queries/Bio::DB::Biblio::soap' ],
 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::Biblio::IO::medlinexml' ],
 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             . 'Bio::DB::Biblio::eutils'
 192     ],
 193
 194     'XML::Writer' => [
 195         0.4,
 196         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'
 197             . 'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'
 198             . 'Bio::SearchIO::Writer::BSMLResultWriter'
 199     ],
 200
 201     'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ],
 202 );
 203
 204 my $mysql_ok = 0;
 205
 206 my @drivers = available_drivers();
 207
 208 # Set up the Bio::Root::Build object
 209 my $build = Bio::Root::Build->new(
 210     module_name   => 'Bio',
 211     dist_name     => 'BioPerl',
 212     dist_version  => '1.006925',
 213     dist_author   => 'BioPerl Team <bioperl-l@bioperl.org>',
 214     dist_abstract => 'Bioinformatics Toolkit',
 215     license       => 'perl',
 216     requires      => {
 217         'perl'       => '5.6.1',
 218         'IO::String' => 0,               # why is this required?
 219         'Data::Stag' => 0.11,            # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 220         'Scalar::Util' => 0,             # not in Perl 5.6.1, arrived in core in 5.7.3
 221         'ExtUtils::Manifest' => '1.52',  # allows spaces in file names
 222     },
 223
 224     build_requires => {
 225         'CPAN'          => 1.81,
 226         'Module::Build' => 0.2805,
 227         'Test::Harness' => 2.62,
 228         'Test::Most'    => 0,
 229         'URI::Escape'   => 0
 230     },
 231
 232     recommends => {
 233         # reverted to a simple Module::Build-compatible hash, but we keep
 234         # additional data in the %recommends hash above. May be converted to
 235         # something simpler if there aren't complaints down the line.
 236         map { $_ => $recommends{$_}[0] } sort keys %recommends
 237     },
 238
 239     get_options => {
 240         accept => {},
 241         network => {} # say 'perl Build.PL --network' to manually request network tests
 242     },
 243
 244     auto_features => {
 245         'EntrezGene' => {
 246             description => "Presence of Bio::ASN1::EntrezGene",
 247             requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 248         },
 249
 250         'DB_File Tests' => {
 251             description => "BDB tests for Bio::DB::SeqFeature::Store",
 252             requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 253         },
 254
 255         'Bio::DB::GFF Tests' => {
 256             description =>
 257                 "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 258             requires => { 'DBI' => 0 },
 259         },
 260
 261         'MySQL Tests' => {
 262             description =>
 263                 "MySQL-related tests for Bio::DB::SeqFeature::Store",
 264             requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
 265         },
 266
 267         'Pg Tests' => {
 268             description =>
 269                 "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 270             requires => { 'DBI' => 0, 'DBD::Pg' => 0 },
 271         },
 272
 273         'SQLite Tests' => {
 274             description =>
 275                 "SQLite-related tests for Bio::DB::SeqFeature::Store",
 276             requires => { 'DBI' => 0, 'DBD::SQLite' => 0 },
 277         },
 278
 279         'Network Tests' => {
 280             description => "Enable tests that need an internet connection",
 281             requires    => { 'LWP::UserAgent' => 0 },
 282         }
 283     },
 284     dynamic_config       => 1,
 285     recursive_test_files => 1,
 286
 287     # Extra files needed for BioPerl modules
 288     xml_files => {
 289         './Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'
 290     },
 291
 292 #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 293 #script_files       => [] # scripts in scripts directory are installed on-demand
 294 );
 295
 296 my $accept = $build->args('accept');
 297
 298 my $proceed = prompt_for_biodb($accept)
 299     if $build->feature('Bio::DB::GFF')
 300     || $build->feature('MySQL Tests')
 301     || $build->feature('Pg Tests')
 302     || $build->feature('SQLite Tests');
 303
 304 # Handle auto features
 305 if ( $proceed && $build->feature('DB_File Tests') ) {
 306
 307     # will return without doing anything if user chose not to run tests during
 308     make_bdb_test();
 309 }
 310 if ($proceed
 311     && (   $build->feature('MySQL Tests')
 312         || $build->feature('Pg Tests')
 313         || $build->feature('SQLite Tests') )
 314     ) {
 315     make_dbi_test();
 316 }
 317
 318 # Ask questions
 319 $build->choose_scripts($accept);
 320
 321 if ( $build->args('network') ) {
 322     if ( $build->feature('Network Tests') ) {
 323         $build->notes( network => 1 );
 324         $build->log_info("  - will run internet-requiring tests\n");
 325     } else {
 326         $build->notes( network => 0 );
 327         $build->log_info(
 328             "  - Missing LWP::UserAgent, can't run network tests\n");
 329     }
 330 } else {
 331     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 332 }
 333
 334 # Add additional files here
 335 $build->add_build_element('xml');
 336
 337 # Create the build script and exit
 338 $build->create_build_script;
 339
 340 exit;
 341
 342 ########################## Helper subs ##########################
 343
 344 sub make_bdb_test {
 345     my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 346     my $path  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature_BDB.t' );
 347     unlink($path) if ( -e $path );
 348     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 349     print $F <<END;
 350 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 351 END
 352     close $F;
 353     $build->add_to_cleanup($path);
 354
 355     #$build->add_to_manifest_skip($path);
 356 }
 357
 358 sub available_drivers {
 359     eval { require DBI; 1; }; # if not installed, this sub won't actually be called
 360     return if $@;
 361     @drivers = DBI->available_drivers;
 362     unless ( grep {/mysql|Pg|SQLite/i} @drivers ) {
 363         $mysql_ok = 0;
 364         return
 365             "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 366     }
 367     $mysql_ok = 1;
 368     return @drivers;
 369 }
 370
 371 sub make_dbi_test {
 372     my $dsn = $build->notes('test_dsn') || return;
 373     my $path0  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 374     my $driver = $build->notes('dbd_driver');
 375     my $path   = File::Spec->catfile( 't', 'LocalDB',
 376           ( $driver eq 'mysql' )  ? 'SeqFeature_mysql.t'
 377         : ( $driver eq 'SQLite' ) ? 'SeqFeature_SQLite.t'
 378         :                           'SeqFeature_Pg.t' );
 379     my $test_db = $build->notes('test_db');
 380     my $user    = $build->notes('test_user');
 381     my $pass    = $build->notes('test_pass');
 382     open my $F, '>', $path
 383         or die "Could not write file '$path' for DBI test: $!\n";
 384     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 385     $str .= " -user $user"     if $user;
 386     $str .= " -password $pass" if $pass;
 387     print $F <<END;
 388 system '$^X $str';
 389 END
 390     close $F;
 391     $build->add_to_cleanup($path);
 392     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 393
 394     #$build->add_to_manifest_skip($path);
 395 }
 396
 397 sub test_biodbgff {
 398     eval { require DBI; }; # if not installed, this sub won't actually be called
 399     return if $@;
 400     @drivers = DBI->available_drivers;
 401     unless ( grep {/mysql|Pg|Oracle/i} @drivers ) {
 402         return "MySQL, Pg nor Oracle DBI drivers are installed";
 403     }
 404     return;
 405 }
 406
 407 sub prompt_for_biodb {
 408     my $accept = shift;
 409     my $proceed = $accept ? 0 : $build->y_n(
 410         "Do you want to run the Bio::DB::GFF or "
 411             . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
 412         'n'
 413     );
 414
 415     if ($proceed) {
 416         my @driver_choices;
 417         foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
 418             if ( grep {/$poss/i} @drivers ) {
 419                 my $choice = $poss;
 420                 $choice =~ s/^(.)/[$1]/;
 421                 push( @driver_choices, $choice );
 422             }
 423         }
 424
 425         my $driver;
 426         if ( @driver_choices > 1 ) {
 427             my ($default) = $driver_choices[0] =~ /\[(.)/;
 428             $driver = $build->prompt(
 429                 "Which database driver should be used? "
 430                     . join( " ", @driver_choices ),
 431                 $default
 432             );
 433         } else {
 434             ($driver) = $driver_choices[0] =~ /\[(.)/;
 435         }
 436         if ( $driver =~ /^[mM]/ ) {
 437             $driver = 'mysql';
 438         } elsif ( $driver =~ /^[pP]/ ) {
 439             $driver = 'Pg';
 440         } elsif ( $driver =~ /^[oO]/ ) {
 441             $driver = 'Oracle';
 442         } elsif ( $driver =~ /^[sS]/ ) {
 443             $driver = 'SQLite';
 444         }
 445
 446         my $test_db = $build->prompt(
 447             "Which database should I use for testing the $driver driver?\n"
 448                 . "This database should already be present but doesn't have to "
 449                 . "be preloaded for any schema",
 450             'test'
 451         );
 452         my $test_host = $build->prompt(
 453             "On which host is database '$test_db' running (hostname, ip address or host:port)",
 454             'localhost'
 455         );
 456         my $test_user = $build->prompt(
 457             "User name for connecting to database '$test_db'?", 'undef' );
 458         my $test_pass = $build->prompt(
 459             "Password for connecting to database '$test_db'?", 'undef' );
 460
 461         my $use_host = 1;
 462         if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
 463             $use_host = 0;
 464         }
 465
 466         my $test_dsn;
 467         if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
 468             $test_dsn = "dbi:$driver:dbname=$test_db";
 469             $mysql_ok = 0;
 470         } else {
 471             $test_dsn = "dbi:$driver:database=$test_db";
 472             $mysql_ok = 0;
 473         }
 474         if ($use_host) {
 475             $test_dsn .= ";host=$test_host";
 476         }
 477
 478         $build->notes( dbd_driver => $driver );
 479         $build->notes( test_db    => $test_db );
 480         $build->notes( test_host  => $test_host );
 481         $build->notes(
 482             test_user => $test_user eq 'undef' ? undef : $test_user );
 483         $build->notes(
 484             test_pass => $test_pass eq 'undef' ? undef : $test_pass );
 485         $build->notes( test_dsn => $test_dsn );
 486
 487         $build->log_info(
 488             "  - will run tests with database driver '$driver' and these settings:\n",
 489             "    Database $test_db\n",
 490             "    Host     $test_host\n",
 491             "    DSN      $test_dsn\n",
 492             "    User     $test_user\n",
 493             "    Password $test_pass\n"
 494         );
 495         $build->log_info( "  - will not run the BioDBSeqFeature live "
 496                 . "database tests (requires MySQL or Pg driver)\n" )
 497             unless ( $driver eq 'mysql' or $driver eq 'Pg' );
 498     } else {
 499         $build->log_info(
 500             "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
 501         );
 502     }
 503
 504     $build->log_info("\n");
 505     return $proceed;
 506 }