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 { eval { require XML::SAX; 1; };
  25
  26 unless ($@) {
  27     if (grep {$_->{Name} =~ 'XML::SAX::RTF'} @{XML::SAX->parsers()}) {
  28         warn <<WARN;
  29
  30 ############################# WARNING #############################
  31
  32 XML::SAX::RTF is not XML::SAX-compliant but is registered as an
  33 XML::SAX parser.  If used as the primary parser, modules requiring
  34 XML::SAX will NOT work. Please install another XML::SAX-compliant
  35 module and modify your local ParserDetails.ini file per XML::SAX
  36 docs to remove references to XML::SAX::RTF.
  37
  38 ############################# WARNING #############################
  39
  40 WARN
  41     sleep 2;
  42     }
  43 }
  44
  45 }
  46
  47 my %recommends = (
  48     # AcePerl support is deprecated, per LDS - cjfields - 5-5-2011
  49
  50     #'Ace'                       => [0,
  51     #    'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'],
  52
  53     'Algorithm::Munkres'        => [0,
  54         'Phylogenetic Networks/Bio::PhyloNetwork'],
  55
  56     'Array::Compare'            => [0,
  57         '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'                => [0,
  68         'NeXML related modules/Bio::AlignIO::nexml,Bio::Nexml::Factory,'.
  69         'Bio::SeqIO::nexml,Bio::TreeIO::nexml'],
  70
  71     'Clone'                     => [0,
  72         'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3'],
  73
  74     'Convert::Binary::C'        => [0,
  75         'Strider functionality/Bio::SeqIO::strider'],
  76
  77     'DB_File'                   => [0,
  78         'Database functionality/Bio::Assemby,Bio::DB'],
  79
  80     'Error'                     => [0,
  81         'OO-based exception handling (very optional)/Bio::Root::Exception'],
  82
  83     'GD'                        => [0,
  84         'Alignment graphic output/Bio::Align::Graphics'],
  85
  86     'Graph'                     => [0.50,
  87         'Phylogenetic Networks, ontology engine implementation, contig analysis'.
  88         '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'.
  89         'Bio::Assembly::Tools::ContigSpectrum'],
  90
  91     'GraphViz'                  => [0,
  92         'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz'],
  93
  94     'HTML::Entities'            => [0,
  95         'Remote analysis POST submissions/Bio::SearchIO::blastxml'],
  96
  97     'HTML::HeadParser'          => [3,
  98         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'],
  99
 100     'HTML::TableExtract'        => [0,
 101         'Parsing HTML tables/Bio::DB::SeqVersion::gi'],
 102
 103     'HTTP::Request::Common'     => [0,
 104         'GenBank+GenPept sequence retrieval, remote http Blast jobs'.
 105         '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'.
 106         'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'],
 107
 108     'Inline::C'                => [0.67,
 109         'Speeding up code like Fasta Bio::DB::Fasta'],
 110
 111     'IO::Scalar'               => [0,
 112         'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'],
 113
 114     'List::MoreUtils'           => [0,
 115         'Back- or reverse-translation of sequences/'.
 116         'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'],
 117
 118     'LWP::UserAgent'            => [0,
 119         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'],
 120
 121     'PostScript::TextBlock'     => [0,
 122         'EPS output/Bio::Tree::Draw::Cladogram'],
 123
 124     'Set::Scalar'               => [0,
 125         'Proper operation/Bio::Tree::Compatible'],
 126
 127     'SOAP::Lite'                => [0,
 128         'Bibliographic queries/Bio::DB::Biblio::soap'],
 129
 130     'Sort::Naturally'           => [0,
 131         'Sort lexically, but sort numeral parts numerically/'.
 132         'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'],
 133
 134     'Spreadsheet::ParseExcel'   => [0,
 135         'Parsing Excel files/Bio::SeqIO::excel'],
 136
 137     'Storable'                  => [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     'SVG'                       => [2.26,
 143         'Creating SVG images/Bio::Draw::Pictogram'],
 144
 145     'SVG::Graph'                => [0.01,
 146         'Creating SVG images/Bio::TreeIO::svggraph'],
 147
 148     'Text::ParseWords'          => [0,
 149         'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'],
 150
 151     'XML::DOM'                  => [0,
 152         'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro'],
 153
 154     'XML::DOM::XPath'           => [0,
 155         'Parsing XML/Bio::SeqIO::interpro'],
 156
 157     'XML::LibXML'               => [0,
 158         'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml'],
 159
 160     'XML::Parser'               => [0,
 161         'Parsing XML/Bio::Biblio::IO::medlinexml'],
 162
 163     'XML::Parser::PerlSAX'      => [0,
 164         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 165         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'],
 166
 167     'XML::SAX'                  => [0.15,
 168         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'],
 169
 170     'XML::SAX::Writer'          => [0,
 171         'Writing XML/Bio::SeqIO::tigrxml'],
 172
 173     'XML::Simple'               => [0,
 174         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'],
 175
 176     'XML::Twig'                 => [0,
 177         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'.
 178         'Bio::DB::Biblio::eutils'],
 179
 180     'XML::Writer'               => [0.4,
 181         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'.
 182         'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'.
 183         'Bio::SearchIO::Writer::BSMLResultWriter'],
 184
 185     'YAML'                      => [0,
 186         'GenBank->GFF3/bp_genbank2gff3.pl'],
 187 );
 188
 189 my $mysql_ok = 0;
 190
 191 my @drivers = available_drivers();
 192
 193 # Set up the Bio::Root::Build object
 194 my $build = Bio::Root::Build->new(
 195     module_name         => 'Bio',
 196     dist_name           => 'BioPerl',
 197     dist_version        => '1.006925',
 198     dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
 199     dist_abstract       => 'Bioinformatics Toolkit',
 200     license             => 'perl',
 201     requires            => {
 202                             'perl'                      => '5.6.1',
 203                             'IO::String'                => 0,    # why is this required?
 204                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 205                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
 206                             'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
 207                            },
 208
 209     build_requires      => {
 210                             'CPAN'                      => 1.81,
 211                             'Module::Build'             => 0.2805,
 212                             'Test::Harness'             => 2.62,
 213                             'Test::Most'                => 0,
 214                             'URI::Escape'               => 0
 215                            },
 216
 217     recommends          => {
 218         # reverted to a simple Module::Build-compatible hash, but we keep
 219         # additional data in the %recommends hash above. May be converted to
 220         # something simpler if there aren't complaints down the line.
 221         map {$_ => $recommends{$_}[0]} sort keys %recommends
 222     },
 223
 224     get_options         => {
 225         accept  => { },
 226         network => { } # say 'perl Build.PL --network' to manually request network tests
 227                            },
 228
 229     auto_features       => {
 230         'EntrezGene'    => {
 231             description => "Presence of Bio::ASN1::EntrezGene",
 232             requires    => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 233         },
 234
 235         'DB_File Tests' => {
 236             description => "BDB tests for Bio::DB::SeqFeature::Store",
 237             requires    => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 238          },
 239
 240         'Bio::DB::GFF Tests' => {
 241             description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 242             requires    => { 'DBI' => 0 },
 243          },
 244
 245         'MySQL Tests'   => {
 246             description => "MySQL-related tests for Bio::DB::SeqFeature::Store",
 247             requires    => { 'DBI' => 0, 'DBD::mysql' => 0 },
 248          },
 249
 250         'Pg Tests'      => {
 251             description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 252             requires    => { 'DBI' => 0, 'DBD::Pg' => 0},
 253          },
 254
 255         'SQLite Tests'  => {
 256             description => "SQLite-related tests for Bio::DB::SeqFeature::Store",
 257             requires    => { 'DBI' => 0, 'DBD::SQLite' => 0},
 258          },
 259
 260         'Network Tests' => {
 261             description => "Enable tests that need an internet connection",
 262             requires    => { 'LWP::UserAgent' => 0 },
 263         }
 264                            },
 265     dynamic_config      => 1,
 266     recursive_test_files => 1,
 267
 268     # Extra files needed for BioPerl modules
 269     xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'},
 270
 271     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 272     #script_files       => [] # scripts in scripts directory are installed on-demand
 273 );
 274
 275 my $accept = $build->args('accept');
 276
 277 my $proceed = prompt_for_biodb($accept)
 278     if $build->feature('Bio::DB::GFF') || $build->feature('MySQL Tests') ||
 279       $build->feature('Pg Tests')      || $build->feature('SQLite Tests');
 280
 281 # Handle auto features
 282 if ($proceed && $build->feature('DB_File Tests')) {
 283     # will return without doing anything if user chose not to run tests during
 284     make_bdb_test();
 285 }
 286 if ($proceed && ($build->feature('MySQL Tests') ||
 287                  $build->feature('Pg Tests') ||
 288                  $build->feature('SQLite Tests'))) {
 289     make_dbi_test();
 290 }
 291
 292 # Ask questions
 293 $build->choose_scripts($accept);
 294
 295 if ($build->args('network')) {
 296     if ($build->feature('Network Tests')) {
 297         $build->notes(network => 1);
 298         $build->log_info("  - will run internet-requiring tests\n");
 299     }
 300     else {
 301         $build->notes(network => 0);
 302         $build->log_info("  - Missing LWP::UserAgent, can't run network tests\n");
 303     }
 304 }
 305 else {
 306     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 307 }
 308
 309 # Add additional files here
 310 $build->add_build_element('xml');
 311
 312 # Create the build script and exit
 313 $build->create_build_script;
 314
 315 exit;
 316
 317 ########################## Helper subs ##########################
 318
 319 sub make_bdb_test {
 320     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 321     my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t');
 322     unlink($path) if (-e $path);
 323     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 324     print $F <<END;
 325 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 326 END
 327     close $F;
 328     $build->add_to_cleanup($path);
 329     #$build->add_to_manifest_skip($path);
 330 }
 331
 332 sub available_drivers {
 333     eval {require DBI; 1;};  # if not installed, this sub won't actually be called
 334     return if $@;
 335     @drivers = DBI->available_drivers;
 336     unless (grep {/mysql|Pg|SQLite/i} @drivers) {
 337         $mysql_ok = 0;
 338         return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 339     }
 340     $mysql_ok = 1;
 341     return @drivers;
 342 }
 343
 344 sub make_dbi_test {
 345     my $dsn = $build->notes('test_dsn') || return;
 346     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 347     my $driver = $build->notes('dbd_driver');
 348     my $path = File::Spec->catfile('t', 'LocalDB',
 349                 ($driver eq 'mysql')   ? 'SeqFeature_mysql.t'  :
 350                 ($driver eq 'SQLite')  ? 'SeqFeature_SQLite.t'  :
 351                 'SeqFeature_Pg.t');
 352     my $test_db = $build->notes('test_db');
 353     my $user = $build->notes('test_user');
 354     my $pass = $build->notes('test_pass');
 355     open my $F, '>', $path or die "Could not write file '$path' for DBI test: $!\n";
 356     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 357     $str .= " -user $user" if $user;
 358     $str .= " -password $pass" if $pass;
 359     print $F <<END;
 360 system '$^X $str';
 361 END
 362     close $F;
 363     $build->add_to_cleanup($path);
 364     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 365     #$build->add_to_manifest_skip($path);
 366 }
 367
 368 sub test_biodbgff {
 369     eval {require DBI;};  # if not installed, this sub won't actually be called
 370     return if $@;
 371     @drivers = DBI->available_drivers;
 372     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 373         return "MySQL, Pg nor Oracle DBI drivers are installed";
 374     }
 375     return;
 376 }
 377
 378 sub prompt_for_biodb {
 379     my $accept = shift;
 380     my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
 381                               "Bio::DB::SeqFeature::Store live database tests? ".
 382                               "y/n", 'n');
 383
 384     if ($proceed) {
 385         my @driver_choices;
 386         foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
 387             if (grep {/$poss/i} @drivers) {
 388                 my $choice = $poss;
 389                 $choice =~ s/^(.)/[$1]/;
 390                 push(@driver_choices, $choice);
 391             }
 392         }
 393
 394         my $driver;
 395         if (@driver_choices > 1) {
 396             my ($default) = $driver_choices[0] =~ /\[(.)/;
 397             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 398         }
 399         else {
 400             ($driver) = $driver_choices[0] =~ /\[(.)/;
 401         }
 402         if ($driver =~ /^[mM]/) {
 403             $driver = 'mysql';
 404         }
 405         elsif ($driver =~ /^[pP]/) {
 406             $driver = 'Pg';
 407         }
 408         elsif ($driver =~ /^[oO]/) {
 409             $driver = 'Oracle';
 410         }
 411         elsif ($driver =~ /^[sS]/) {
 412             $driver = 'SQLite';
 413         }
 414
 415         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
 416                                      "This database should already be present but doesn't have to ".
 417                                      "be preloaded for any schema", 'test');
 418         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 419         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 420         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 421
 422         my $use_host = 1;
 423         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 424             $use_host = 0;
 425         }
 426
 427         my $test_dsn;
 428         if ($driver eq 'Pg' || $driver eq 'SQLite') {
 429             $test_dsn = "dbi:$driver:dbname=$test_db";
 430             $mysql_ok = 0;
 431         }
 432         else {
 433             $test_dsn = "dbi:$driver:database=$test_db";
 434             $mysql_ok = 0;
 435         }
 436         if ($use_host) {
 437             $test_dsn .= ";host=$test_host";
 438         }
 439
 440         $build->notes(dbd_driver => $driver);
 441         $build->notes(test_db => $test_db);
 442         $build->notes(test_host => $test_host);
 443         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 444         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 445         $build->notes(test_dsn => $test_dsn);
 446
 447         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 448                         "    Database $test_db\n",
 449                         "    Host     $test_host\n",
 450                         "    DSN      $test_dsn\n",
 451                         "    User     $test_user\n",
 452                         "    Password $test_pass\n");
 453         $build->log_info("  - will not run the BioDBSeqFeature live ".
 454                          "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
 455     }
 456     else {
 457         $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
 458     }
 459
 460     $build->log_info("\n");
 461     return $proceed;
 462 }