Build.PL

   1 #!/usr/bin/perl -w
   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 #      http://bugzilla.open-bio.org/show_bug.cgi?id=2975
  23
  24 {
  25
  26 eval {
  27     require XML::SAX;
  28     1;
  29 };
  30
  31 unless ($@) {
  32     if (grep {$_->{Name} =~ 'XML::SAX::RTF'} @{XML::SAX->parsers()}) {
  33         warn <<WARN;
  34 ############################# WARNING #############################
  35
  36 XML::SAX::RTF is not XML::SAX-compliant but is registered as an
  37 XML::SAX parser.  If used as the primary parser, modules requiring
  38 XML::SAX will NOT work.  Please install another XML::SAX-compliant
  39 module and modify your local ParserDetails.ini file per XML::SAX docs
  40 to remove references to XML::SAX::RTF.
  41
  42 ############################# WARNING #############################
  43 WARN
  44     sleep 3;
  45     }
  46 }
  47
  48 }
  49
  50 our @drivers;
  51
  52 my $mysql_ok = 0;
  53
  54 # Set up the Bio::Root::Build object
  55 my $build = Bio::Root::Build->new(
  56     module_name         => 'Bio',
  57     dist_name           => 'BioPerl',
  58     dist_version_from   => 'Bio/Root/Version.pm',
  59     dist_author         => 'BioPerl Team <bioperl-l@bioperl.org>',
  60     dist_abstract       => 'Bioinformatics Toolkit',
  61     license             => 'perl',
  62     no_index            => {'dir'                       => [qw(examples/root/lib)]},
  63     requires            => {
  64                             'perl'                      => '5.6.1',
  65                             'IO::String'                => 0,
  66                             'DB_File'                   => 0,
  67                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
  68                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
  69                             'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
  70                            },
  71     build_requires      => {
  72                             'Test::More'                => 0,
  73                             'Module::Build'             => 0.2805,
  74                             'Test::Harness'             => 2.62,
  75                             'CPAN'                      => 1.81
  76                            },
  77     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
  78                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
  79                             'Algorithm::Munkres'        => '0/Phylogenetic Networks/Bio::PhyloNetwork',
  80                             'Array::Compare'            => '0/Phylogenetic Networks/Bio::PhyloNetwork',
  81                             # this won't actually install due to circular dep, but we have no way of doing a post-install
  82                             # the [circular dependency!] specifies it is only installed on explicit request for this specific module,
  83                             # not when simply choosing to install 'all' modules
  84                             'Bio::ASN1::EntrezGene'     => '0/parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]',
  85                             'Clone'                     => '0/cloning objects/Bio::Tools::Primer3',
  86                             'Convert::Binary::C'        => '0/strider functionality/Bio::SeqIO::strider',
  87                             'Graph'                     => '0/Phylogenetic Networks, ontology engine implementation, contig analysis/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,Bio::Assembly::Tools::ContigSpectrum',
  88                             'GraphViz'                  => '0/Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz',
  89                             'HTML::Entities'            => '0/remote analysis POST submissions/Bio::SearchIO::blastxml',
  90                             'HTML::HeadParser'          => '3/parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder',
  91                             'HTTP::Request::Common'     => '0/GenBank+GenPept sequence retrieval, remote http Blast jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*',
  92                             'List::MoreUtils'           => '0/Back- or reverse-translation of sequences/Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate',
  93                             'LWP::UserAgent'            => '0/remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent',
  94                             'Math::Random'              => '0/Random Phylogenetic Networks/Bio::PhyloNetwork::RandomFactory',
  95                             'PostScript::TextBlock'     => '0/EPS output/Bio::Tree::Draw::Cladogram',
  96                             'Set::Scalar'               => '0/proper operation/Bio::Tree::Compatible',
  97                             'SOAP::Lite'                => '0/Bibliographic queries/Bio::DB::Biblio::soap',
  98                             'Sort::Naturally'           => '0/sort lexically, but sort numeral parts numerically/Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr',
  99                             'Spreadsheet::ParseExcel'   => '0/parsing Excel files/Bio::SeqIO::excel',
 100                             'Storable'                  => '2.05/storing sequence objects in local file cache/Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb',
 101                             'SVG'                       => '2.26/creating SVG images/Bio::Draw::Pictogram',
 102                             'SVG::Graph'                => '0.01/creating SVG images/Bio::TreeIO::svggraph',
 103                             'Text::ParseWords'          => '0/test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader',
 104                             'URI::Escape'               => '0/dealing with web resources/Bio::FeatureIO::gff,Bio::FeatureIO::interpro,Bio::DB::Biblio::eutils,Bio::DB::EUtilParameters,Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated',
 105                             'XML::DOM::XPath'           => '0.13/parsing interpro features/Bio::FeatureIO::interpro',
 106                             'XML::Parser'               => '0/parsing xml/Bio::Biblio::IO::medlinexml',
 107                             'XML::Parser::PerlSAX'      => '0/parsing xml/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp',
 108                             'XML::SAX'                  => '0.15/parsing xml/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
 109                             'XML::SAX::Writer'          => '0/writing xml/Bio::SeqIO::tigrxml',
 110                             'XML::Simple'               => '0/reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery',
 111                             'XML::Twig'                 => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils',
 112                             'XML::Writer'               => '0.4/parsing and writing xml/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,Bio::SearchIO::Writer::BSMLResultWriter',
 113     },
 114     get_options         => {
 115                             accept  => { },
 116                             network => { } # say 'perl Build.PL --network' to manually request network tests
 117                            },
 118     auto_features       => {
 119                             BioDBSeqFeature_BDB   => {
 120                                                         description      => "BDB tests for Bio::DB::SeqFeature::Store",
 121                                                         feature_requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
 122                                                      },
 123                             BioDBGFF              => {
 124                                                         description      => "BioDBGFF database tests (will need to answer questions before really enabling)",
 125                                                         feature_requires => { 'DBI' => 0 },
 126                                                         excludes_os      => ['mswin'],
 127                                                         test             => \&test_biodbgff # Bio::Root::Build unique requirement that after everything else succeeds, supplied code ref must also return undef
 128                                                      },
 129                             BioDBSeqFeature_mysql => {
 130                                                         description      => "MySQL tests for Bio::DB::SeqFeature::Store",
 131                                                         feature_requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
 132                                                         test             => \&test_db_sf
 133                                                      },
 134                             BioDBSeqFeature_Pg    => {
 135                                                         description      => "Postgres tests for Bio::DB::SeqFeature::Store",
 136                                                         feature_requires => { 'DBI' => 0, 'DBD::Pg' => 0},
 137                                                         test             => \&test_db_sf
 138                                                      },
 139                             BioDBSeqFeature_SQLite    => {
 140                                                         description      => "SQLite tests for Bio::DB::SeqFeature::Store",
 141                                                         feature_requires => { 'DBI' => 0, 'DBD::SQLite' => 0},
 142                                                         test             => \&test_db_sf
 143                                                      },
 144                             Network               => {
 145                                                         description      => "Enable tests that need an internet connection",
 146                                                         feature_requires => { 'LWP::UserAgent' => 0 },
 147                                                         test             => \&Bio::Root::Build::test_internet
 148                                                      }
 149                            },
 150     dynamic_config      => 1,
 151     create_makefile_pl  => 'passthrough',
 152     recursive_test_files => 1,
 153     # Extra files needed for BioPerl modules
 154     xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'},
 155
 156     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 157     #script_files       => [] # scripts in scripts directory are installed on-demand
 158 );
 159
 160 my $accept = $build->args->{accept};
 161
 162 my $proceed = prompt_for_biodb($accept) if $build->feature('BioDBGFF') || $build->feature('BioDBSeqFeature_mysql');
 163
 164 # Handle auto features
 165 if ($proceed && $build->feature('BioDBSeqFeature_BDB')) {
 166     # will return without doing anything if user chose not to run tests during
 167     # prompt_for_biodb() above
 168     make_bdb_test();
 169 }
 170 if ($proceed && ($build->feature('BioDBSeqFeature_mysql') or $build->feature('BioDBSeqFeature_Pg'))) {
 171     make_dbi_test();
 172 }
 173
 174 # Ask questions
 175 $build->choose_scripts($accept);
 176 #prompt_for_biodbgff($accept) if $build->feature('BioDBGFF');
 177 {
 178     if ($build->args('network')) {
 179         if ($build->feature('Network')) {
 180             $build->notes(network => 1);
 181             $build->log_info("  - will run internet-requiring tests\n");
 182         }
 183         else {
 184             $build->notes(network => 0);
 185             $build->log_info("  - will not run network tests since I seem to be missing essential network functionality\n");
 186         }
 187     }
 188     else {
 189         $build->prompt_for_network($accept) if $build->feature('Network');
 190     }
 191     # then in test script:
 192     #   use Bio::Root::Build;
 193     #   my $build = Module::Build->current;
 194     #   my $do_network_tests = $build->notes('network');
 195 }
 196
 197 # Request that some scripts run post-installation
 198 $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
 199
 200 # Add extra things to MANIFEST.SKIP
 201 $build->add_to_manifest_skip('bioperl.lisp');
 202
 203 # Add additional files here
 204 $build->add_build_element('xml');
 205
 206 # Create the build script and exit
 207 $build->create_build_script;
 208
 209 exit;
 210
 211 sub make_bdb_test {
 212     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 213     my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t');
 214     unlink($path) if (-e $path);
 215     open(my $F, ">", $path) || die "Can't create test file\n";
 216     print $F <<END;
 217 system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
 218 END
 219     close $F;
 220     $build->add_to_cleanup($path);
 221     $build->add_to_manifest_skip($path);
 222 }
 223
 224 sub test_db_sf {
 225     eval {require DBI;};  # if not installed, this sub won't actually be called
 226     @drivers = DBI->available_drivers;
 227     unless (grep {/mysql|Pg|SQLite/i} @drivers) {
 228         $mysql_ok = 0;
 229         return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests";
 230     }
 231     $mysql_ok = 1;
 232     return;
 233 }
 234
 235 sub make_dbi_test {
 236     my $dsn = $build->notes('test_dsn') || return;
 237     my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
 238     my $driver = $build->notes('dbd_driver');
 239     my $path = File::Spec->catfile('t', 'LocalDB',
 240                 ($driver eq 'mysql')   ? 'SeqFeature_mysql.t'  :
 241                 ($driver eq 'SQLite')  ? 'SeqFeature_SQLite.t'  :
 242                 'SeqFeature_Pg.t');
 243     my $test_db = $build->notes('test_db');
 244     my $user = $build->notes('test_user');
 245     my $pass = $build->notes('test_pass');
 246     open my $F,">$path";
 247     my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn $dsn";
 248     $str .= " -user $user" if $user;
 249     $str .= " -password $pass" if $pass;
 250     print $F <<END;
 251 system '$^X $str';
 252 END
 253     close $F;
 254     $build->add_to_cleanup($path);
 255     $build->add_to_cleanup($test_db) if $driver eq 'SQLite';
 256     $build->add_to_manifest_skip($path);
 257 }
 258
 259 sub test_biodbgff {
 260     eval {require DBI;};  # if not installed, this sub won't actually be called
 261     @drivers = DBI->available_drivers;
 262     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 263         return "MySQL, Pg nor Oracle DBI drivers are installed";
 264     }
 265     return;
 266 }
 267
 268 sub prompt_for_biodb {
 269     my $accept = shift;
 270     my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
 271                               "Bio::DB::SeqFeature::Store live database tests? ".
 272                               "y/n", 'n');
 273
 274     if ($proceed) {
 275         my @driver_choices;
 276         foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
 277             if (grep {/$poss/i} @drivers) {
 278                 my $choice = $poss;
 279                 $choice =~ s/^(.)/[$1]/;
 280                 push(@driver_choices, $choice);
 281             }
 282         }
 283
 284         my $driver;
 285         if (@driver_choices > 1) {
 286             my ($default) = $driver_choices[0] =~ /\[(.)/;
 287             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 288         }
 289         else {
 290             ($driver) = $driver_choices[0] =~ /\[(.)/;
 291         }
 292         if ($driver =~ /^[mM]/) {
 293             $driver = 'mysql';
 294         }
 295         elsif ($driver =~ /^[pP]/) {
 296             $driver = 'Pg';
 297         }
 298         elsif ($driver =~ /^[oO]/) {
 299             $driver = 'Oracle';
 300         }
 301         elsif ($driver =~ /^[sS]/) {
 302             $driver = 'SQLite';
 303         }
 304
 305         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
 306                                      "This database should already be present but doesn't have to ".
 307                                      "be preloaded for any schema", 'test');
 308         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 309         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 310         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 311
 312         my $use_host = 1;
 313         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 314             $use_host = 0;
 315         }
 316
 317         my $test_dsn;
 318         if ($driver eq 'Pg' || $driver eq 'SQLite') {
 319             $test_dsn = "dbi:$driver:dbname=$test_db";
 320             $mysql_ok = 0;
 321         }
 322         else {
 323             $test_dsn = "dbi:$driver:database=$test_db";
 324             $mysql_ok = 0;
 325         }
 326         if ($use_host) {
 327             $test_dsn .= ";host=$test_host";
 328         }
 329
 330         $build->notes(dbd_driver => $driver);
 331         $build->notes(test_db => $test_db);
 332         $build->notes(test_host => $test_host);
 333         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 334         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 335         $build->notes(test_dsn => $test_dsn);
 336
 337         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 338                         "    Database $test_db\n",
 339                         "    Host     $test_host\n",
 340                         "    DSN      $test_dsn\n",
 341                         "    User     $test_user\n",
 342                         "    Password $test_pass\n");
 343         $build->log_info("  - will not run the BioDBSeqFeature live ".
 344                          "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg');
 345     }
 346     else {
 347         $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
 348     }
 349
 350     $build->log_info("\n");
 351     return $proceed;
 352 }