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     'Clone'                     => [0,
  68         'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3'],
  69
  70     'Convert::Binary::C'        => [0,
  71         'Strider functionality/Bio::SeqIO::strider'],
  72
  73     'Error'                     => [0,
  74         'OO-based exception handling (very optional)/Bio::Root::Exception'],
  75
  76     'GD'                        => [0,
  77         'Alignment graphic output/Bio::Align::Graphics'],
  78
  79     'Graph'                     => [0.50,
  80         'Phylogenetic Networks, ontology engine implementation, contig analysis'.
  81         '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'.
  82         'Bio::Assembly::Tools::ContigSpectrum'],
  83
  84     'GraphViz'                  => [0,
  85         'Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz'],
  86
  87     'HTML::Entities'            => [0,
  88         'Remote analysis POST submissions/Bio::SearchIO::blastxml'],
  89
  90     'HTML::HeadParser'          => [3,
  91         'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'],
  92
  93     'HTML::TableExtract'        => [0,
  94         'Parsing HTML tables/Bio::DB::SeqVersion::gi'],
  95
  96     'HTTP::Request::Common'     => [0,
  97         'GenBank+GenPept sequence retrieval, remote http Blast jobs'.
  98         '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'.
  99         'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'],
 100
 101     'List::MoreUtils'           => [0,
 102         'Back- or reverse-translation of sequences/'.
 103         'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'],
 104
 105     'LWP::UserAgent'            => [0,
 106         'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'],
 107
 108     'Math::Random'              => [0,
 109         'Random Phylogenetic Networks/Bio::PhyloNetwork::RandomFactory'],
 110
 111     'PostScript::TextBlock'     => [0,
 112         'EPS output/Bio::Tree::Draw::Cladogram'],
 113
 114     'Set::Scalar'               => [0,
 115         'Proper operation/Bio::Tree::Compatible'],
 116
 117     'SOAP::Lite'                => [0,
 118         'Bibliographic queries/Bio::DB::Biblio::soap'],
 119
 120     'Sort::Naturally'           => [0,
 121         'Sort lexically, but sort numeral parts numerically/'.
 122         'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'],
 123
 124     'Spreadsheet::ParseExcel'   => [0,
 125         'Parsing Excel files/Bio::SeqIO::excel'],
 126
 127     'Storable'                  => [2.05,
 128         'Storing sequence objects in local file cache/'.
 129         'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'.
 130         'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'],
 131
 132     'SVG'                       => [2.26,
 133         'Creating SVG images/Bio::Draw::Pictogram'],
 134
 135     'SVG::Graph'                => [0.01,
 136         'Creating SVG images/Bio::TreeIO::svggraph'],
 137
 138     'Text::ParseWords'          => [0,
 139         'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'],
 140
 141     'XML::DOM::XPath'           => [0.13,
 142         'parsing interpro features/Bio::FeatureIO::interpro'],
 143
 144     'XML::Parser'               => [0,
 145         'parsing xml/Bio::Biblio::IO::medlinexml'],
 146
 147     'XML::Parser::PerlSAX'      => [0,
 148         'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
 149         'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'],
 150
 151     'XML::SAX'                  => [0.15,
 152         'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'],
 153
 154     'XML::SAX::Writer'          => [0,
 155         'Writing XML/Bio::SeqIO::tigrxml'],
 156
 157     'XML::Simple'               => [0,
 158         'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'],
 159
 160     'XML::Twig'                 => [0,
 161         'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'.
 162         'Bio::DB::Biblio::eutils'],
 163
 164     'XML::Writer'               => [0.4,
 165         'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'.
 166         'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'.
 167         'Bio::SearchIO::Writer::BSMLResultWriter'],
 168
 169     'YAML'                      => [0,
 170         'GenBank->GFF3/bp_genbank2gff3.pl'],
 171 );
 172
 173 my $mysql_ok = 0;
 174
 175 my @drivers = available_drivers();
 176
 177 # Set up the Bio::Root::Build object
 178 my $build = Bio::Root::Build->new(
 179     module_name         => 'Bio',
 180     dist_name           => 'BioPerl',
 181     dist_version_from   => 'Bio/Root/Version.pm',
 182     dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
 183     dist_abstract       => 'Bioinformatics Toolkit',
 184     license             => 'perl',
 185     no_index            => {'dir'       => [qw(examples/root/lib)]},
 186     requires            => {
 187                             'perl'                      => '5.6.1',
 188                             'IO::String'                => 0,    # why is this required?
 189                             'DB_File'                   => 0,    # why is this required?
 190                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
 191                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
 192                             'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
 193                            },
 194
 195     build_requires      => {
 196                             'CPAN'                      => 1.81,
 197                             'Module::Build'             => 0.2805,
 198                             'Test::Harness'             => 2.62,
 199                             'Test::Most'                => 0,
 200                             'URI::Escape'               => 0
 201                            },
 202
 203     recommends          => {
 204         # reverted to a simple Module::Build-compatible hash, but we keep
 205         # additional data in the %recommends hash above. May be converted to
 206         # something simpler if there aren't complaints down the line.
 207         map {$_ => $recommends{$_}[0]} sort keys %recommends
 208     },
 209
 210     get_options         => {
 211         accept  => { },
 212         network => { } # say 'perl Build.PL --network' to manually request network tests
 213                            },
 214
 215     auto_features       => {
 216         'EntrezGene'    => {
 217             description => "Presence of Bio::ASN1::EntrezGene",
 218             requires    => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 219         },
 220
 221         'DB_File Tests' => {
 222             description => "BDB tests for Bio::DB::SeqFeature::Store",
 223             requires    => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 224          },
 225
 226         'Bio::DB::GFF Tests' => {
 227             description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
 228             requires    => { 'DBI' => 0 },
 229          },
 230
 231         'MySQL Tests'   => {
 232             description => "MySQL-related tests for Bio::DB::SeqFeature::Store",
 233             requires    => { 'DBI' => 0, 'DBD::mysql' => 0 },
 234          },
 235
 236         'Pg Tests'      => {
 237             description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
 238             requires    => { 'DBI' => 0, 'DBD::Pg' => 0},
 239          },
 240
 241         'SQLite Tests'  => {
 242             description => "SQLite-related tests for Bio::DB::SeqFeature::Store",
 243             requires    => { 'DBI' => 0, 'DBD::SQLite' => 0},
 244          },
 245
 246         'Network Tests' => {
 247             description => "Enable tests that need an internet connection",
 248             requires    => { 'LWP::UserAgent' => 0 },
 249         }
 250                            },
 251     dynamic_config      => 1,
 252     #create_makefile_pl  => 'passthrough',
 253     recursive_test_files => 1,
 254
 255     # Extra files needed for BioPerl modules
 256     xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'},
 257
 258     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 259     #script_files       => [] # scripts in scripts directory are installed on-demand
 260 );
 261
 262 my $accept = $build->args('accept');
 263
 264 # how much do I hate this?  Let me count the ways.....
 265 if (!$build->feature('EntrezGene')) {
 266     warn <<WARN;
 267 ############################# WARNING #############################
 268
 269 Bio::ASN1::EntrezGene not found. This is an *optional* module;
 270 however, because it has a circular dependency with BioPerl we do not
 271 include it on our list of recommended modules.
 272
 273 If you require EntrezGene functionality, you can install
 274 Bio::ASN1::EntrezGene after BioPerl has finished installing.
 275
 276 ############################# WARNING #############################
 277
 278 WARN
 279     sleep 3;
 280 }
 281
 282 my $proceed = prompt_for_biodb($accept)
 283     if $build->feature('Bio::DB::GFF') || $build->feature('MySQL Tests') ||
 284       $build->feature('Pg Tests')      || $build->feature('SQLite Tests');
 285
 286 # Handle auto features
 287 if ($proceed && $build->feature('DB_File Tests')) {
 288     # will return without doing anything if user chose not to run tests during
 289     make_bdb_test();
 290 }
 291 if ($proceed && ($build->feature('MySQL Tests') ||
 292                  $build->feature('Pg Tests') ||
 293                  $build->feature('SQLite Tests'))) {
 294     make_dbi_test();
 295 }
 296
 297 # Ask questions
 298 $build->choose_scripts($accept);
 299
 300 if ($build->args('network')) {
 301     if ($build->feature('Network Tests')) {
 302         $build->notes(network => 1);
 303         $build->log_info("  - will run internet-requiring tests\n");
 304     }
 305     else {
 306         $build->notes(network => 0);
 307         $build->log_info("  - Missing LWP::UserAgent, can't run network tests\n");
 308     }
 309 }
 310 else {
 311     $build->prompt_for_network($accept) if $build->feature('Network Tests');
 312 }
 313
 314 # Add additional files here
 315 $build->add_build_element('xml');
 316
 317 # Create the build script and exit
 318 $build->create_build_script;
 319
 320 exit;
 321
 322 ########################## Helper subs ##########################
 323
 324 sub make_bdb_test {
 325     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 326     my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t');
 327     unlink($path) if (-e $path);
 328     open(my $F, ">", $path) || die "Can't create test file\n";
 329     print $F <<END;
 330 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 331 END
 332     close $F;
 333     $build->add_to_cleanup($path);
 334     #$build->add_to_manifest_skip($path);
 335 }
 336
 337 sub available_drivers {
 338     eval {require DBI; 1;};  # if not installed, this sub won't actually be called
 339     return if $@;
 340     @drivers = DBI->available_drivers;
 341     unless (grep {/mysql|Pg|SQLite/i} @drivers) {
 342         $mysql_ok = 0;
 343         return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 344     }
 345     $mysql_ok = 1;
 346     return @drivers;
 347 }
 348
 349 sub make_dbi_test {
 350     my $dsn = $build->notes('test_dsn') || return;
 351     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 352     my $driver = $build->notes('dbd_driver');
 353     my $path = File::Spec->catfile('t', 'LocalDB',
 354                 ($driver eq 'mysql')   ? 'SeqFeature_mysql.t'  :
 355                 ($driver eq 'SQLite')  ? 'SeqFeature_SQLite.t'  :
 356                 'SeqFeature_Pg.t');
 357     my $test_db = $build->notes('test_db');
 358     my $user = $build->notes('test_user');
 359     my $pass = $build->notes('test_pass');
 360     open my $F,">$path";
 361     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\"";
 362     $str .= " -user $user" if $user;
 363     $str .= " -password $pass" if $pass;
 364     print $F <<END;
 365 system '$^X $str';
 366 END
 367     close $F;
 368     $build->add_to_cleanup($path);
 369     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 370     #$build->add_to_manifest_skip($path);
 371 }
 372
 373 sub test_biodbgff {
 374     eval {require DBI;};  # if not installed, this sub won't actually be called
 375     return if $@;
 376     @drivers = DBI->available_drivers;
 377     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 378         return "MySQL, Pg nor Oracle DBI drivers are installed";
 379     }
 380     return;
 381 }
 382
 383 sub prompt_for_biodb {
 384     my $accept = shift;
 385     my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
 386                               "Bio::DB::SeqFeature::Store live database tests? ".
 387                               "y/n", 'n');
 388
 389     if ($proceed) {
 390         my @driver_choices;
 391         foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
 392             if (grep {/$poss/i} @drivers) {
 393                 my $choice = $poss;
 394                 $choice =~ s/^(.)/[$1]/;
 395                 push(@driver_choices, $choice);
 396             }
 397         }
 398
 399         my $driver;
 400         if (@driver_choices > 1) {
 401             my ($default) = $driver_choices[0] =~ /\[(.)/;
 402             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 403         }
 404         else {
 405             ($driver) = $driver_choices[0] =~ /\[(.)/;
 406         }
 407         if ($driver =~ /^[mM]/) {
 408             $driver = 'mysql';
 409         }
 410         elsif ($driver =~ /^[pP]/) {
 411             $driver = 'Pg';
 412         }
 413         elsif ($driver =~ /^[oO]/) {
 414             $driver = 'Oracle';
 415         }
 416         elsif ($driver =~ /^[sS]/) {
 417             $driver = 'SQLite';
 418         }
 419
 420         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
 421                                      "This database should already be present but doesn't have to ".
 422                                      "be preloaded for any schema", 'test');
 423         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 424         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 425         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 426
 427         my $use_host = 1;
 428         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 429             $use_host = 0;
 430         }
 431
 432         my $test_dsn;
 433         if ($driver eq 'Pg' || $driver eq 'SQLite') {
 434             $test_dsn = "dbi:$driver:dbname=$test_db";
 435             $mysql_ok = 0;
 436         }
 437         else {
 438             $test_dsn = "dbi:$driver:database=$test_db";
 439             $mysql_ok = 0;
 440         }
 441         if ($use_host) {
 442             $test_dsn .= ";host=$test_host";
 443         }
 444
 445         $build->notes(dbd_driver => $driver);
 446         $build->notes(test_db => $test_db);
 447         $build->notes(test_host => $test_host);
 448         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 449         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 450         $build->notes(test_dsn => $test_dsn);
 451
 452         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 453                         "    Database $test_db\n",
 454                         "    Host     $test_host\n",
 455                         "    DSN      $test_dsn\n",
 456                         "    User     $test_user\n",
 457                         "    Password $test_pass\n");
 458         $build->log_info("  - will not run the BioDBSeqFeature live ".
 459                          "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
 460     }
 461     else {
 462         $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
 463     }
 464
 465     $build->log_info("\n");
 466     return $proceed;
 467 }