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