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 ModuleBuildBioperl that
   7 # doesn't get installed
   8
   9 # In the future developers may need to alter the requires and recommends and
  10 # possibly Network sections of ModuleBuildBioperl->new() below, but otherwise
  11 # nothing else here is likely to need changing.
  12
  13 use strict;
  14 use ModuleBuildBioperl;
  15
  16 our @drivers;
  17
  18 my $mysql_ok = 0;
  19
  20 # Set up the ModuleBuildBioperl object
  21 my $build = ModuleBuildBioperl->new(
  22     module_name         => 'Bio',
  23     dist_name           => 'bioperl',
  24     dist_version_from   => 'Bio/Root/Version.pm',
  25     dist_author         => 'Bioperl Team <bioperl-l@bioperl.org>',
  26     dist_abstract       => 'Bioinformatics Toolkit',
  27     license             => 'perl',
  28     requires            => {
  29                             'perl'                      => '5.6.1',
  30                             'IO::String'                => 0,
  31                             'DB_File'                   => 0,
  32                             'Data::Stag'                => 0.10, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
  33                             'Scalar::Util'              => 0 # not in Perl 5.6.1, arrived in core in 5.7.3
  34                            },
  35     build_requires      => {
  36                             'Test::More'                => 0,
  37                             'Module::Build'             => 0.2805,
  38                             'Test::Harness'             => 2.62,
  39                             'CPAN'                      => 1.81
  40                            },
  41     recommends          => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
  42                             'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
  43                             # this won't actually install due to circular dep, but we have no way of doing a post-install
  44                             'Bio::ASN1::EntrezGene'     => '0/parsing entrezgene/Bio::SeqIO::entrezgene',
  45                             # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
  46                             'Class::AutoClass'          => '1/creating objects/Bio::Graph::SimpleGraph,Bio::Graph::SimpleGraph::Traversal,Bio::Graph::ProteinGraph',
  47                             'Clone'                     => '0/cloning objects/Bio::Graph::ProteinGraph,Bio::Tools::Primer3',
  48                             'Convert::Binary::C'        => '0/strider functionality/Bio::SeqIO::strider',
  49                             # part of Data::Stag, which is now required above (note the default use of Data::Stag in BioPerl does not require XML::Parser::PerlSAX)
  50                             #'Data::Stag::XMLWriter'     => '0/writing choas xml files/Bio::SeqIO::chaosxml',
  51                             'GD'                        => '1.3/rendering Sequences and Features/Bio::Graphics::Glyph*',
  52                             'GD::SVG'                   => '0/creating SVG images/Bio::Graphics::Panel',
  53                             # we specifically want Graph::Directed, but that has no VERSION
  54                             'Graph'                     => '0/ontology engine implementation for the GO parser/Bio::Ontology::SimpleGOEngine::GraphAdaptor,Bio::PhyloNetwork',
  55                             'HTML::Entities'            => '0/remote analysis POST submissions/Bio::SearchIO::blastxml',
  56                             'HTML::Parser'              => '3/screen scraping www.gdb.org/Bio::DB::GDB',
  57                             '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*',
  58                             'LWP::UserAgent'            => '0/remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::Tools::WebBlat,Bio::WebAgent,Bio::Graphics::Glyph::image',
  59                             'PostScript::TextBlock'     => '0/EPS output/Bio::Tree::Draw::Cladogram',
  60                             'Set::Scalar'               => '0/proper operation/Bio::Tree::Compatible',
  61                             'SOAP::Lite'                => '0/XEMBL Services and Bibliographic queries/Bio::DB::XEMBLService,Bio::DB::Biblio::soap',
  62                             'Spreadsheet::ParseExcel'   => '0/parsing Excel files/Bio::SeqIO::excel',
  63                             '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',
  64                             'SVG'                       => '2.26/SVG output/Bio::Graphics::Pictogram',
  65                             'SVG::Graph'                => '0.01/creating SVG images/Bio::TreeIO::svggraph',
  66                             'Text::Parsewords'          => '0/test scripts/Bio::Graphics',
  67                             'URI::Escape'               => '0/dealing with web resources/Bio::Tools::WebBlat,Bio::FeatureIO::gff,Bio::FeatureIO::interpro,Bio::DB::Biblio::eutils,Bio::DB::EUtilities::Cookie,Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated',
  68                             'XML::DOM::XPath'           => '0.13/parsing interpro features/Bio::FeatureIO::interpro',
  69                             'XML::Parser'               => '0/parsing xml/Bio::Biblio::IO::medlinexml',
  70                             'XML::Parser::PerlSAX'      => '0/parsing xml/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp',
  71                             'XML::SAX'                  => '0.15/parsing xml/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax',
  72                             'XML::SAX::Writer'          => '0/writing xml/Bio::SeqIO::tigrxml',
  73                             'XML::Twig'                 => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils,Bio::Graph::IO::psi_xml',
  74                             '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',
  75                             'Math::Random'          => '0/Random Phylogenetic Networks/Bio::PhyloNetwork::RandomFactory',
  76                             'Algorithm::Munkres'    => '0/Phylogenetic Networks/Bio::PhyloNetwork',
  77                             'Array::Compare'        => '0/Phylogenetic Networks/Bio::PhyloNetwork',
  78                             'GraphViz'              => '0/Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz',
  79     },
  80     get_options         => {
  81                             network => { } # say 'perl Build.PL --network' to manually request network tests
  82                            },
  83     auto_features       => {
  84                             BioDBSeqFeature_BDB   => {
  85                                                         description      => "BDB tests for Bio::DB::SeqFeature::Store",
  86                                                         feature_requires => { 'DB_File' => 0 } # feature_requires is like requires, execpt that it doesn't trigger installation
  87                                                      },
  88                             BioDBGFF              => {
  89                                                         description      => "BioDBGFF database tests (will need to answer questions before really enabling)",
  90                                                         feature_requires => { 'DBI' => 0 },
  91                                                         excludes_os      => ['mswin'],
  92                                                         test             => \&test_biodbgff # ModuleBuildBioperl unique requirement that after everything else succeeds, supplied code ref must also return undef
  93                                                      },
  94                             BioDBSeqFeature_mysql => {
  95                                                         description      => "MySQL tests for Bio::DB::SeqFeature::Store",
  96                                                         feature_requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
  97                                                         test             => \&test_db_sf
  98                                                      },
  99                             Network               => {
 100                                                         description => "Enable tests that need an internet connection",
 101                                                         requires    => { 'LWP::UserAgent' => 0 },
 102                                                         test        => \&ModuleBuildBioperl::test_internet
 103                                                      }
 104                            },
 105     dynamic_config      => 1,
 106     create_makefile_pl  => 'passthrough'
 107
 108     #pm_files           => {} # modules in Bio are treated as if they were in lib and auto-installed
 109     #script_files       => [] # scripts in scripts directory are installed on-demand
 110 );
 111
 112 my $accept = $build->args->{accept};
 113
 114 prompt_for_biodb($accept) if $build->feature('BioDBGFF') || $build->feature('BioDBSeqFeature_mysql');
 115
 116 # Handle auto features
 117 if ($build->feature('BioDBSeqFeature_BDB') && $mysql_ok) {
 118     # will return without doing anything if user chose not to run tests during
 119     # prompt_for_biodb() above
 120     make_bdb_test();
 121 }
 122 if ($build->feature('BioDBSeqFeature_mysql')) {
 123     make_dbi_test();
 124 }
 125
 126 # Ask questions
 127 $build->choose_scripts($accept);
 128 #prompt_for_biodbgff($accept) if $build->feature('BioDBGFF');
 129 {
 130     if ($build->args('network')) {
 131         if ($build->feature('Network')) {
 132             $build->notes(network => 1);
 133             $build->log_info("  - will run internet-requiring tests\n");
 134         }
 135         else {
 136             $build->notes(network => 0);
 137             $build->log_info("  - will not run network tests since I seem to be missing essential network functionality\n");
 138         }
 139     }
 140     else {
 141         prompt_for_network($accept) if $build->feature('Network');
 142     }
 143     # then in test script:
 144     #   use Module::Build;
 145     #   my $build = Module::Build->current;
 146     #   my $do_network_tests = $build->notes('network');
 147 }
 148
 149 # Request that some scripts run post-installation
 150 $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
 151
 152 # Add extra things to MANIFEST.SKIP
 153 $build->add_to_manifest_skip('bioperl.lisp', 'Bio/Tools/WebBlat.pm');
 154
 155 # Create the build script and exit
 156 $build->create_build_script;
 157
 158 exit;
 159
 160
 161 sub make_bdb_test {
 162     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 163     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_BDB.t');
 164     unlink($path) if (-e $path);
 165     open(my $F, ">", $path) || die "Can't create test file\n";
 166     print $F <<END;
 167 system 'perl $path0 -adaptor berkeleydb -create 1 -temp 1';
 168 END
 169     close $F;
 170     $build->add_to_cleanup($path);
 171     $build->add_to_manifest_skip($path);
 172 }
 173
 174 sub test_db_sf {
 175     eval {require DBI;};  # if not installed, this sub won't actually be called
 176     @drivers = DBI->available_drivers;
 177     unless (grep {/mysql/i} @drivers) {
 178         $mysql_ok = 0;
 179         return "Only MySQL DBI driver supported for BioDBSeqFeature_mysql tests";
 180     }
 181     $mysql_ok = 1;
 182     return;
 183 }
 184
 185 sub make_dbi_test {
 186     my $dsn = $build->notes('test_dsn') || return;
 187     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 188     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_mysql.t');
 189     my $test_db = $build->notes('test_db');
 190     my $user = $build->notes('test_user');
 191     my $pass = $build->notes('test_pass');
 192     open my $F,">$path";
 193     my $str = "$path0 -adaptor DBI::mysql -create 1 -temp 1 -dsn $dsn";
 194     $str .= " -user $user" if $user;
 195     $str .= " -password $pass" if $pass;
 196     print $F <<END;
 197     system 'perl $str';
 198 END
 199     close $F;
 200     $build->add_to_cleanup($path);
 201     $build->add_to_manifest_skip($path);
 202 }
 203
 204 sub test_biodbgff {
 205     eval {require DBI;};  # if not installed, this sub won't actually be called
 206     @drivers = DBI->available_drivers;
 207     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 208         return "MySQL, Pg nor Oracle DBI drivers are installed";
 209     }
 210     return;
 211 }
 212
 213 sub prompt_for_biodb {
 214     my $accept = shift;
 215     my $proceed = $accept ? 0 : $build->y_n("Do you want to run the BioDBGFF or ".
 216                               "BioDBSeqFeature_mysql live database tests? ".
 217                               "y/n", 'n');
 218
 219     if ($proceed) {
 220         my @driver_choices;
 221         foreach my $poss ('mysql', 'Pg', 'Oracle') {
 222             if (grep {/$poss/i} @drivers) {
 223                 my $choice = $poss;
 224                 $choice =~ s/^(.)/[$1]/;
 225                 push(@driver_choices, $choice);
 226             }
 227         }
 228
 229         my $driver;
 230         if (@driver_choices > 1) {
 231             my ($default) = $driver_choices[0] =~ /\[(.)/;
 232             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 233         }
 234         else {
 235             ($driver) = $driver_choices[0] =~ /\[(.)/;
 236         }
 237         if ($driver =~ /^[mM]/) {
 238             $driver = 'mysql';
 239         }
 240         elsif ($driver =~ /^[pP]/) {
 241             $driver = 'Pg';
 242         }
 243         elsif ($driver =~ /^[oO]/) {
 244             $driver = 'Oracle';
 245         }
 246
 247         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?", 'test');
 248         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 249         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 250         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 251
 252         my $use_host = 1;
 253         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 254             $use_host = 0;
 255         }
 256
 257         my $test_dsn;
 258         if ($driver eq 'Pg') {
 259             $test_dsn = "dbi:$driver:dbname=$test_db";
 260             $mysql_ok = 0;
 261         }
 262         else {
 263             $test_dsn = "dbi:$driver:database=$test_db";
 264             $mysql_ok = 0;
 265         }
 266         if ($use_host) {
 267             $test_dsn .= ";host=$test_host";
 268         }
 269
 270         $build->notes(dbd_driver => $driver);
 271         $build->notes(test_db => $test_db);
 272         $build->notes(test_host => $test_host);
 273         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 274         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 275         $build->notes(test_dsn => $test_dsn);
 276
 277         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 278                         "    Database $test_db\n",
 279                         "    Host     $test_host\n",
 280                         "    DSN      $test_dsn\n",
 281                         "    User     $test_user\n",
 282                         "    Password $test_pass\n");
 283         $build->log_info("  - will not run the BioDBSeqFeature_mysql live ".
 284                          "database tests (requires MySQL driver)\n") unless $mysql_ok;
 285     }
 286     else {
 287         $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
 288     }
 289
 290     $build->log_info("\n");
 291 }
 292
 293 sub prompt_for_network {
 294     my $accept = shift;
 295
 296     my $proceed = $accept
 297                 ? 0 :$build->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
 298
 299     if ($proceed) {
 300         $build->notes(network => 1);
 301         $build->log_info("  - will run internet-requiring tests\n");
 302     }
 303     else {
 304         $build->notes(network => 0);
 305         $build->log_info("  - will not run internet-requiring tests\n");
 306     }
 307 }