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     'IO::Scalar'               => [0,
 109         'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'],
 110
 111     'List::MoreUtils'           => [0,
 112         'Back- or reverse-translation of sequences/'.
 113         'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'],
 114
 115     'LWP::UserAgent'            => [0,
 116         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'],
 117
 118     'PostScript::TextBlock'     => [0,
 119         'EPS output/Bio::Tree::Draw::Cladogram'],
 120
 121     'Set::Scalar'               => [0,
 122         'Proper operation/Bio::Tree::Compatible'],
 123
 124     'SOAP::Lite'                => [0,
 125         'Bibliographic queries/Bio::DB::Biblio::soap'],
 126
 127     'Sort::Naturally'           => [0,
 128         'Sort lexically, but sort numeral parts numerically/'.
 129         'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'],
 130
 131     'Spreadsheet::ParseExcel'   => [0,
 132         'Parsing Excel files/Bio::SeqIO::excel'],
 133
 134     'Storable'                  => [2.05,
 135         'Storing sequence objects in local file cache/'.
 136         'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'.
 137         'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'],
 138
 139     'SVG'                       => [2.26,
 140         'Creating SVG images/Bio::Draw::Pictogram'],
 141
 142     'SVG::Graph'                => [0.01,
 143         'Creating SVG images/Bio::TreeIO::svggraph'],
 144
 145     'Text::ParseWords'          => [0,
 146         'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'],
 147
 148     'XML::DOM'                  => [0,
 149         'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro'],
 150
 151     'XML::DOM::XPath'           => [0,
 152         'Parsing XML/Bio::SeqIO::interpro'],
 153
 154     'XML::LibXML'               => [0,
 155         'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml'],
 156
 157     'XML::Parser'               => [0,
 158         'Parsing XML/Bio::Biblio::IO::medlinexml'],
 159
 160     'XML::Parser::PerlSAX'      => [0,
 161         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 162         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'],
 163
 164     'XML::SAX'                  => [0.15,
 165         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'],
 166
 167     'XML::SAX::Writer'          => [0,
 168         'Writing XML/Bio::SeqIO::tigrxml'],
 169
 170     'XML::Simple'               => [0,
 171         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'],
 172
 173     'XML::Twig'                 => [0,
 174         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'.
 175         'Bio::DB::Biblio::eutils'],
 176
 177     'XML::Writer'               => [0.4,
 178         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'.
 179         'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'.
 180         'Bio::SearchIO::Writer::BSMLResultWriter'],
 181
 182     'YAML'                      => [0,
 183         'GenBank->GFF3/bp_genbank2gff3.pl'],
 184 );
 185
 186 my $mysql_ok = 0;
 187
 188 my @drivers = available_drivers();
 189
 190 # Set up the Bio::Root::Build object
 191 my $build = Bio::Root::Build->new(
 192     module_name         => 'Bio',
 193     dist_name           => 'BioPerl',
 194     dist_version        => '1.006924',
 195     dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
 196     dist_abstract       => 'Bioinformatics Toolkit',
 197     license             => 'perl',
 198     requires            => {
 199                             'perl'                      => '5.6.1',
 200                             'IO::String'                => 0,    # why is this required?
 201                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 202                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
 203                             'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
 204                            },
 205
 206     build_requires      => {
 207                             'CPAN'                      => 1.81,
 208                             'Module::Build'             => 0.2805,
 209                             'Test::Harness'             => 2.62,
 210                             'Test::Most'                => 0,
 211                             'URI::Escape'               => 0
 212                            },
 213
 214     recommends          => {
 215         # reverted to a simple Module::Build-compatible hash, but we keep
 216         # additional data in the %recommends hash above. May be converted to
 217         # something simpler if there aren't complaints down the line.
 218         map {$_ => $recommends{$_}[0]} sort keys %recommends
 219     },
 220
 221     get_options         => {
 222         accept  => { },
 223         network => { } # say 'perl Build.PL --network' to manually request network tests
 224                            },
 225
 226     auto_features       => {
 227         'EntrezGene'    => {
 228             description => "Presence of Bio::ASN1::EntrezGene",
 229             requires    => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 230         },
 231
 232         'DB_File Tests' => {
 233             description => "BDB tests for Bio::DB::SeqFeature::Store",
 234             requires    => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 235          },
 236
 237         'Bio::DB::GFF Tests' => {
 238             description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 239             requires    => { 'DBI' => 0 },
 240          },
 241
 242         'MySQL Tests'   => {
 243             description => "MySQL-related tests for Bio::DB::SeqFeature::Store",
 244             requires    => { 'DBI' => 0, 'DBD::mysql' => 0 },
 245          },
 246
 247         'Pg Tests'      => {
 248             description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 249             requires    => { 'DBI' => 0, 'DBD::Pg' => 0},
 250          },
 251
 252         'SQLite Tests'  => {
 253             description => "SQLite-related tests for Bio::DB::SeqFeature::Store",
 254             requires    => { 'DBI' => 0, 'DBD::SQLite' => 0},
 255          },
 256
 257         'Network Tests' => {
 258             description => "Enable tests that need an internet connection",
 259             requires    => { 'LWP::UserAgent' => 0 },
 260         }
 261                            },
 262     dynamic_config      => 1,
 263     #create_makefile_pl  => 'passthrough',
 264     recursive_test_files => 1,
 265
 266     # Extra files needed for BioPerl modules
 267     xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'},
 268
 269     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 270     #script_files       => [] # scripts in scripts directory are installed on-demand
 271 );
 272
 273 my $accept = $build->args('accept');
 274
 275 # how much do I hate this?  Let me count the ways.....
 276 #if (!$build->feature('EntrezGene')) {
 277 #    warn <<WARN;
 278 ############################## WARNING #############################
 279 #
 280 #Bio::ASN1::EntrezGene not found. This is an *optional* module;
 281 #however, because it has a circular dependency with BioPerl we do not
 282 #include it on our list of recommended modules.
 283 #
 284 #If you require EntrezGene functionality, you can install
 285 #Bio::ASN1::EntrezGene after BioPerl has finished installing.
 286 #
 287 ############################## WARNING #############################
 288 #
 289 #WARN
 290 #    sleep 3;
 291 #}
 292
 293 my $proceed = prompt_for_biodb($accept)
 294     if $build->feature('Bio::DB::GFF') || $build->feature('MySQL Tests') ||
 295       $build->feature('Pg Tests')      || $build->feature('SQLite Tests');
 296
 297 # Handle auto features
 298 if ($proceed && $build->feature('DB_File Tests')) {
 299     # will return without doing anything if user chose not to run tests during
 300     make_bdb_test();
 301 }
 302 if ($proceed && ($build->feature('MySQL Tests') ||
 303                  $build->feature('Pg Tests') ||
 304                  $build->feature('SQLite Tests'))) {
 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     }
 316     else {
 317         $build->notes(network => 0);
 318         $build->log_info("  - Missing LWP::UserAgent, can't run network tests\n");
 319     }
 320 }
 321 else {
 322     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 323 }
 324
 325 # Add additional files here
 326 $build->add_build_element('xml');
 327
 328 # Create the build script and exit
 329 $build->create_build_script;
 330
 331 exit;
 332
 333 ########################## Helper subs ##########################
 334
 335 sub make_bdb_test {
 336     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 337     my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t');
 338     unlink($path) if (-e $path);
 339     open my $F, '>', $path or die "Could not write test file '$path': $!\n";
 340     print $F <<END;
 341 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 342 END
 343     close $F;
 344     $build->add_to_cleanup($path);
 345     #$build->add_to_manifest_skip($path);
 346 }
 347
 348 sub available_drivers {
 349     eval {require DBI; 1;};  # if not installed, this sub won't actually be called
 350     return if $@;
 351     @drivers = DBI->available_drivers;
 352     unless (grep {/mysql|Pg|SQLite/i} @drivers) {
 353         $mysql_ok = 0;
 354         return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 355     }
 356     $mysql_ok = 1;
 357     return @drivers;
 358 }
 359
 360 sub make_dbi_test {
 361     my $dsn = $build->notes('test_dsn') || return;
 362     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 363     my $driver = $build->notes('dbd_driver');
 364     my $path = File::Spec->catfile('t', 'LocalDB',
 365                 ($driver eq 'mysql')   ? 'SeqFeature_mysql.t'  :
 366                 ($driver eq 'SQLite')  ? 'SeqFeature_SQLite.t'  :
 367                 'SeqFeature_Pg.t');
 368     my $test_db = $build->notes('test_db');
 369     my $user = $build->notes('test_user');
 370     my $pass = $build->notes('test_pass');
 371     open my $F, '>', $path or die "Could not write file '$path' for DBI test: $!\n";
 372     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 373     $str .= " -user $user" if $user;
 374     $str .= " -password $pass" if $pass;
 375     print $F <<END;
 376 system '$^X $str';
 377 END
 378     close $F;
 379     $build->add_to_cleanup($path);
 380     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 381     #$build->add_to_manifest_skip($path);
 382 }
 383
 384 sub test_biodbgff {
 385     eval {require DBI;};  # if not installed, this sub won't actually be called
 386     return if $@;
 387     @drivers = DBI->available_drivers;
 388     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 389         return "MySQL, Pg nor Oracle DBI drivers are installed";
 390     }
 391     return;
 392 }
 393
 394 sub prompt_for_biodb {
 395     my $accept = shift;
 396     my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
 397                               "Bio::DB::SeqFeature::Store live database tests? ".
 398                               "y/n", 'n');
 399
 400     if ($proceed) {
 401         my @driver_choices;
 402         foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
 403             if (grep {/$poss/i} @drivers) {
 404                 my $choice = $poss;
 405                 $choice =~ s/^(.)/[$1]/;
 406                 push(@driver_choices, $choice);
 407             }
 408         }
 409
 410         my $driver;
 411         if (@driver_choices > 1) {
 412             my ($default) = $driver_choices[0] =~ /\[(.)/;
 413             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 414         }
 415         else {
 416             ($driver) = $driver_choices[0] =~ /\[(.)/;
 417         }
 418         if ($driver =~ /^[mM]/) {
 419             $driver = 'mysql';
 420         }
 421         elsif ($driver =~ /^[pP]/) {
 422             $driver = 'Pg';
 423         }
 424         elsif ($driver =~ /^[oO]/) {
 425             $driver = 'Oracle';
 426         }
 427         elsif ($driver =~ /^[sS]/) {
 428             $driver = 'SQLite';
 429         }
 430
 431         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
 432                                      "This database should already be present but doesn't have to ".
 433                                      "be preloaded for any schema", 'test');
 434         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 435         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 436         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 437
 438         my $use_host = 1;
 439         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 440             $use_host = 0;
 441         }
 442
 443         my $test_dsn;
 444         if ($driver eq 'Pg' || $driver eq 'SQLite') {
 445             $test_dsn = "dbi:$driver:dbname=$test_db";
 446             $mysql_ok = 0;
 447         }
 448         else {
 449             $test_dsn = "dbi:$driver:database=$test_db";
 450             $mysql_ok = 0;
 451         }
 452         if ($use_host) {
 453             $test_dsn .= ";host=$test_host";
 454         }
 455
 456         $build->notes(dbd_driver => $driver);
 457         $build->notes(test_db => $test_db);
 458         $build->notes(test_host => $test_host);
 459         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 460         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 461         $build->notes(test_dsn => $test_dsn);
 462
 463         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 464                         "    Database $test_db\n",
 465                         "    Host     $test_host\n",
 466                         "    DSN      $test_dsn\n",
 467                         "    User     $test_user\n",
 468                         "    Password $test_pass\n");
 469         $build->log_info("  - will not run the BioDBSeqFeature live ".
 470                          "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
 471     }
 472     else {
 473         $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
 474     }
 475
 476     $build->log_info("\n");
 477     return $proceed;
 478 }