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     'Algorithm::Munkres' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ],
  51
  52     'Array::Compare' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ],
  53
  54     # this won't actually install due to circular dep, but we have no way of
  55     # doing a post-install the [circular dependency!] specifies it is only
  56     # installed on explicit request for this specific module, not when simply
  57     # choosing to install 'all' modules
  58
  59     #'Bio::ASN1::EntrezGene'     => [0,
  60     #    'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'],
  61
  62     'CGI' => [ 0, 'CGI-y things/Bio::DB::Query::HIVQuery' ],
  63
  64     'Clone' => [ 0, 'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3' ],
  65
  66     'Convert::Binary::C' =>
  67         [ 0, 'Strider functionality/Bio::SeqIO::strider' ],
  68
  69     'DB_File' => [ 0, 'Database functionality/Bio::Assemby,Bio::DB' ],
  70
  71     'Error' => [
  72         0, 'OO-based exception handling (very optional)/Bio::Root::Exception'
  73     ],
  74
  75     'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ],
  76
  77     'Graph' => [
  78         0.50,
  79         'Phylogenetic Networks, ontology engine implementation, contig analysis'
  80             . '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'
  81             . 'Bio::Assembly::Tools::ContigSpectrum'
  82     ],
  83
  84     'GraphViz' => [
  85         0, 'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz'
  86     ],
  87
  88     'HTML::Entities' =>
  89         [ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ],
  90
  91     'HTML::HeadParser' => [
  92         3,
  93         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'
  94     ],
  95
  96     'HTML::TableExtract' =>
  97         [ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ],
  98
  99     'HTTP::Request::Common' => [
 100         0,
 101         'GenBank+GenPept sequence retrieval, remote http Blast jobs'
 102             . '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'
 103             . 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'
 104     ],
 105
 106     'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ],
 107
 108     'IO::Scalar' => [
 109         0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'
 110     ],
 111
 112     'List::MoreUtils' => [
 113         0,
 114         'Back- or reverse-translation of sequences/'
 115             . 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'
 116     ],
 117
 118     'LWP::UserAgent' => [
 119         0,
 120         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'
 121     ],
 122
 123     'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ],
 124
 125     'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],
 126
 127     'Sort::Naturally' => [
 128         0,
 129         'Sort lexically, but sort numeral parts numerically/'
 130             . 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'
 131     ],
 132
 133     'Spreadsheet::ParseExcel' =>
 134         [ 0, 'Parsing Excel files/Bio::SeqIO::excel' ],
 135
 136     'Storable' => [
 137         2.05,
 138         'Storing sequence objects in local file cache/'
 139             . 'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'
 140             . 'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'
 141     ],
 142
 143     'SVG::Graph' => [ 0.01, 'Creating SVG images/Bio::TreeIO::svggraph' ],
 144
 145     'Text::ParseWords' =>
 146         [ 0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader' ],
 147
 148     'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ],
 149
 150     'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ],
 151
 152     'XML::LibXML' =>
 153         [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ],
 154
 155     'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ],
 156
 157     'XML::Parser::PerlSAX' => [
 158         0,
 159         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 160         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'
 161     ],
 162
 163     'XML::SAX' => [
 164         0.15,
 165         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'
 166     ],
 167
 168     'XML::SAX::Writer' => [ 0, 'Writing XML/Bio::SeqIO::tigrxml' ],
 169
 170     'XML::Simple' => [
 171         0,
 172         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'
 173     ],
 174
 175     'XML::Twig' => [
 176         0,
 177         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez'
 178     ],
 179
 180     'XML::Writer' => [
 181         0.4,
 182         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'
 183             . 'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'
 184             . 'Bio::SearchIO::Writer::BSMLResultWriter'
 185     ],
 186
 187     'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ],
 188 );
 189
 190 my $mysql_ok = 0;
 191
 192 my @drivers = available_drivers();
 193
 194 # Set up the Bio::Root::Build object
 195 my $build = Bio::Root::Build->new(
 196     module_name   => 'Bio',
 197     dist_name     => 'BioPerl',
 198     dist_version  => $Bio::Root::Version::VERSION,
 199     dist_author   => 'BioPerl Team <bioperl-l@bioperl.org>',
 200     dist_abstract => 'Bioinformatics Toolkit',
 201     license       => 'perl',
 202     requires      => {
 203         'perl'       => '5.6.1',
 204         'IO::String' => 0,               # why is this required?
 205         'Data::Stag' => 0.11,            # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 206         'Scalar::Util' => 0,             # not in Perl 5.6.1, arrived in core in 5.7.3
 207         'ExtUtils::Manifest' => '1.52',  # allows spaces in file names
 208     },
 209
 210     configure_requires => {
 211         'Module::Build' => 0.42,
 212     },
 213
 214     build_requires => {
 215         'Module::Build' => 0.42,
 216         'CPAN'          => 1.81,
 217         'Test::Harness' => 2.62,
 218         'Test::Most'    => 0,
 219         'URI::Escape'   => 0
 220     },
 221
 222     recommends => {
 223         # reverted to a simple Module::Build-compatible hash, but we keep
 224         # additional data in the %recommends hash above. May be converted to
 225         # something simpler if there aren't complaints down the line.
 226         map { $_ => $recommends{$_}[0] } sort keys %recommends
 227     },
 228
 229     get_options => {
 230         accept => {},
 231         network => {} # say 'perl Build.PL --network' to manually request network tests
 232     },
 233
 234     auto_features => {
 235         'EntrezGene' => {
 236             description => "Presence of Bio::ASN1::EntrezGene",
 237             requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 238         },
 239
 240         'DB_File Tests' => {
 241             description => "BDB tests for Bio::DB::SeqFeature::Store",
 242             requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 243         },
 244
 245         'Bio::DB::GFF Tests' => {
 246             description =>
 247                 "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 248             requires => { 'DBI' => 0 },
 249         },
 250
 251         'MySQL Tests' => {
 252             description =>
 253                 "MySQL-related tests for Bio::DB::SeqFeature::Store",
 254             requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
 255         },
 256
 257         'Pg Tests' => {
 258             description =>
 259                 "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 260             requires => { 'DBI' => 0, 'DBD::Pg' => 0 },
 261         },
 262
 263         'SQLite Tests' => {
 264             description =>
 265                 "SQLite-related tests for Bio::DB::SeqFeature::Store",
 266             requires => { 'DBI' => 0, 'DBD::SQLite' => 0 },
 267         },
 268
 269         'Network Tests' => {
 270             description => "Enable tests that need an internet connection",
 271             requires    => { 'LWP::UserAgent' => 0 },
 272         }
 273     },
 274     dynamic_config       => 1,
 275     recursive_test_files => 1,
 276
 277     # Extra files needed for BioPerl modules
 278     xml_files => {
 279         './Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'
 280     },
 281
 282 #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 283 #script_files       => [] # scripts in scripts directory are installed on-demand
 284 );
 285
 286 my $accept = $build->args('accept');
 287
 288 my $proceed = prompt_for_biodb($accept)
 289     if $build->feature('Bio::DB::GFF')
 290     || $build->feature('MySQL Tests')
 291     || $build->feature('Pg Tests')
 292     || $build->feature('SQLite Tests');
 293
 294 # Handle auto features
 295 if ( $proceed && $build->feature('DB_File Tests') ) {
 296
 297     # will return without doing anything if user chose not to run tests during
 298     make_bdb_test();
 299 }
 300 if ($proceed
 301     && (   $build->feature('MySQL Tests')
 302         || $build->feature('Pg Tests')
 303         || $build->feature('SQLite Tests') )
 304     ) {
 305     make_dbi_test();
 306 }
 307
 308 # Ask questions
 309 $build->choose_scripts($accept);
 310
 311 if ( $build->args('network') ) {
 312     if ( $build->feature('Network Tests') ) {
 313         $build->notes( network => 1 );
 314         $build->log_info("  - will run internet-requiring tests\n");
 315     } else {
 316         $build->notes( network => 0 );
 317         $build->log_info(
 318             "  - Missing LWP::UserAgent, can't run network tests\n");
 319     }
 320 } else {
 321     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 322 }
 323
 324 # Add additional files here
 325 $build->add_build_element('xml');
 326
 327 if ( ! -e 'MANIFEST' ) {
 328     $build->ACTION_manifest();
 329 }
 330
 331 # Create the build script and exit
 332 $build->create_build_script();
 333
 334 exit;
 335
 336 ########################## Helper subs ##########################
 337
 338 sub make_bdb_test {
 339     my $path0 = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 340     my $path  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature_BDB.t' );
 341     unlink($path) if ( -e $path );
 342     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 343     print $F <<END;
 344 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 345 END
 346     close $F;
 347     $build->add_to_cleanup($path);
 348
 349     #$build->add_to_manifest_skip($path);
 350 }
 351
 352 sub available_drivers {
 353     eval { require DBI; 1; }; # if not installed, this sub won't actually be called
 354     return if $@;
 355     @drivers = DBI->available_drivers;
 356     unless ( grep {/mysql|Pg|SQLite/i} @drivers ) {
 357         $mysql_ok = 0;
 358         return
 359             "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 360     }
 361     $mysql_ok = 1;
 362     return @drivers;
 363 }
 364
 365 sub make_dbi_test {
 366     my $dsn = $build->notes('test_dsn') || return;
 367     my $path0  = File::Spec->catfile( 't', 'LocalDB', 'SeqFeature.t' );
 368     my $driver = $build->notes('dbd_driver');
 369     my $path   = File::Spec->catfile( 't', 'LocalDB',
 370           ( $driver eq 'mysql' )  ? 'SeqFeature_mysql.t'
 371         : ( $driver eq 'SQLite' ) ? 'SeqFeature_SQLite.t'
 372         :                           'SeqFeature_Pg.t' );
 373     my $test_db = $build->notes('test_db');
 374     my $user    = $build->notes('test_user');
 375     my $pass    = $build->notes('test_pass');
 376     open my $F, '>', $path
 377         or die "Could not write file '$path' for DBI test: $!\n";
 378     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 379     $str .= " -user $user"     if $user;
 380     $str .= " -password $pass" if $pass;
 381     print $F <<END;
 382 system '$^X $str';
 383 END
 384     close $F;
 385     $build->add_to_cleanup($path);
 386     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 387
 388     #$build->add_to_manifest_skip($path);
 389 }
 390
 391 sub test_biodbgff {
 392     eval { require DBI; }; # if not installed, this sub won't actually be called
 393     return if $@;
 394     @drivers = DBI->available_drivers;
 395     unless ( grep {/mysql|Pg|Oracle/i} @drivers ) {
 396         return "MySQL, Pg nor Oracle DBI drivers are installed";
 397     }
 398     return;
 399 }
 400
 401 sub prompt_for_biodb {
 402     my $accept = shift;
 403     my $proceed = $accept ? 0 : $build->y_n(
 404         "Do you want to run the Bio::DB::GFF or "
 405             . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
 406         'n'
 407     );
 408
 409     if ($proceed) {
 410         my @driver_choices;
 411         foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
 412             if ( grep {/$poss/i} @drivers ) {
 413                 my $choice = $poss;
 414                 $choice =~ s/^(.)/[$1]/;
 415                 push( @driver_choices, $choice );
 416             }
 417         }
 418
 419         my $driver;
 420         if ( @driver_choices > 1 ) {
 421             my ($default) = $driver_choices[0] =~ /\[(.)/;
 422             $driver = $build->prompt(
 423                 "Which database driver should be used? "
 424                     . join( " ", @driver_choices ),
 425                 $default
 426             );
 427         } else {
 428             ($driver) = $driver_choices[0] =~ /\[(.)/;
 429         }
 430         if ( $driver =~ /^[mM]/ ) {
 431             $driver = 'mysql';
 432         } elsif ( $driver =~ /^[pP]/ ) {
 433             $driver = 'Pg';
 434         } elsif ( $driver =~ /^[oO]/ ) {
 435             $driver = 'Oracle';
 436         } elsif ( $driver =~ /^[sS]/ ) {
 437             $driver = 'SQLite';
 438         }
 439
 440         my $test_db = $build->prompt(
 441             "Which database should I use for testing the $driver driver?\n"
 442                 . "This database should already be present but doesn't have to "
 443                 . "be preloaded for any schema",
 444             'test'
 445         );
 446         my $test_host = $build->prompt(
 447             "On which host is database '$test_db' running (hostname, ip address or host:port)",
 448             'localhost'
 449         );
 450         my $test_user = $build->prompt(
 451             "User name for connecting to database '$test_db'?", 'undef' );
 452         my $test_pass = $build->prompt(
 453             "Password for connecting to database '$test_db'?", 'undef' );
 454
 455         my $use_host = 1;
 456         if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
 457             $use_host = 0;
 458         }
 459
 460         my $test_dsn;
 461         if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
 462             $test_dsn = "dbi:$driver:dbname=$test_db";
 463             $mysql_ok = 0;
 464         } else {
 465             $test_dsn = "dbi:$driver:database=$test_db";
 466             $mysql_ok = 0;
 467         }
 468         if ($use_host) {
 469             $test_dsn .= ";host=$test_host";
 470         }
 471
 472         $build->notes( dbd_driver => $driver );
 473         $build->notes( test_db    => $test_db );
 474         $build->notes( test_host  => $test_host );
 475         $build->notes(
 476             test_user => $test_user eq 'undef' ? undef : $test_user );
 477         $build->notes(
 478             test_pass => $test_pass eq 'undef' ? undef : $test_pass );
 479         $build->notes( test_dsn => $test_dsn );
 480
 481         $build->log_info(
 482             "  - will run tests with database driver '$driver' and these settings:\n",
 483             "    Database $test_db\n",
 484             "    Host     $test_host\n",
 485             "    DSN      $test_dsn\n",
 486             "    User     $test_user\n",
 487             "    Password $test_pass\n"
 488         );
 489         $build->log_info( "  - will not run the BioDBSeqFeature live "
 490                 . "database tests (requires MySQL or Pg driver)\n" )
 491             unless ( $driver eq 'mysql' or $driver eq 'Pg' );
 492     } else {
 493         $build->log_info(
 494             "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
 495         );
 496     }
 497
 498     $build->log_info("\n");
 499     return $proceed;
 500 }