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 # Set up the ModuleBuildBioperl object
  19 my $build = ModuleBuildBioperl->new(
  20     module_name         => 'Bio',
  21     dist_name           => 'bioperl',
  22     dist_version_from   => 'Bio/Root/Version.pm',
  23     dist_author         => 'Bioperl Team <bioperl-l@bioperl.org>',
  24     dist_abstract       => 'Bioinformatics Toolkit',
  25     license             => 'artistic',
  26     requires            => {
  27                             'perl'                      => '5.6.1',
  28                             'IO::String'                => 0,
  29                             'DB_File'                   => 0
  30                            },
  31     build_requires      => {
  32                             'Test::More'                => 0,
  33                             'Module::Build'             => 0.2805,
  34                             'Test::Harness'             => 2.62,
  35                             'CPAN'                      => 1.81
  36                            },
  37     recommends          => [ # does what you would expect of recommends, except more informative output and generates optional_features in META.yml
  38                              # also note this is an array of hash refs, as the order is important
  39                             {'Ace'                       => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'},
  40                             # this won't actually install due to circular dep, but we have no way of doing a post-install
  41                             {'Bio::ASN1::EntrezGene'     => '0/parsing entrezgene/Bio::SeqIO::entrezgene'},
  42                             # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
  43                             {'Class::AutoClass'          => '1/creating objects/Bio::Graph::SimpleGraph,Bio::Graph::SimpleGraph::Traversal,Bio::Graph::ProteinGraph'},
  44                             {'Clone'                     => '0/cloning objects/Bio::Graph::ProteinGraph,Bio::Tools::Primer3'},
  45                             {'Convert::Binary::C'        => '0/strider functionality/Bio::SeqIO::strider'},
  46                             {'Data::Stag::XMLWriter'     => '0/writing choas xml files/Bio::SeqIO::chaosxml'},
  47                             {'GD'                        => '1.3/rendering Sequences and Features/Bio::Graphics::Glyph*'},
  48                             {'GD::SVG'                   => '0/creating SVG images/Bio::Graphics::Panel'},
  49                             # we specifically want Graph::Directed, but that has no VERSION
  50                             {'Graph'                     => '0/ontology engine implementation for the GO parser/Bio::Ontology::SimpleGOEngine::GraphAdaptor'},
  51                             {'HTML::Entities'            => '0/remote analysis POST submissions/Bio::SearchIO::blastxml'},
  52                             {'HTML::Parser'              => '3/screen scraping www.gdb.org/Bio::DB::GDB'},
  53                             {'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*'},
  54                             {'LWP::UserAgent'            => '0/remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::Tools::WebBlat,Bio::WebAgent,Bio::Graphics::Glyph::image'},
  55                             {'Set::Scalar'               => '0/proper operation/Bio::Tree::Compatible'},
  56                             {'SOAP::Lite'                => '0/XEMBL Services and Bibliographic queries/Bio::DB::XEMBLService,Bio::DB::Biblio::soap'},
  57                             {'Spreadsheet::ParseExcel'   => '0/parsing Excel files/Bio::SeqIO::excel'},
  58                             {'Storable'                  => '0/storing sequence objects in local file cache/Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb'},
  59                             {'SVG'                       => '2.26/SVG output/Bio::Graphics::Pictogram'},
  60                             {'SVG::Graph'                => '0.01/creating SVG images/Bio::TreeIO::svggraph'},
  61                             {'Text::Shellwords'          => '0/test scripts/Bio::Graphics'},
  62                             {'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'},
  63                             # this is actually just an undeclared req of XML::DOM::XPath v0.12, used by Bio::FeatureIO::interpro
  64                             # should be able to remove this when v0.13 of XML::DOM::XPath is available
  65                             {'XML::XPath'                => '0/parsing xml/XML::DOM::XPath,Bio::FeatureIO::interpro'},
  66                             {'XML::DOM::XPath'           => '0/parsing interpro features/Bio::FeatureIO::interpro'},
  67                             {'XML::Parser'               => '0/parsing xml/Bio::Biblio::IO::medlinexml'},
  68                             {'XML::Parser::PerlSAX'      => '0/parsing xml/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'},
  69                             {'XML::SAX'                  => '0/parsing xml/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'},
  70                             {'XML::SAX::Writer'          => '0/writing xml/Bio::SeqIO::tigrxml'},
  71                             # this is just required by XML::Simple, since installation will fail if only XML::SAX::PurePerl is installed
  72                             # should be able to remove this when XML::SAX is bug-fixed for this problem
  73                             {'XML::SAX::ExpatXS'         => '0/parsing xml/XML::Simple,Bio::DB::EUtilities'},
  74                             {'XML::Simple'               => '0/parsing xml/Bio::DB::EUtilities'},
  75                             {'XML::Twig'                 => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils,Bio::Graph::IO::psi_xml'},
  76                             {'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'}
  77                            ],
  78     get_options         => {
  79                             network => { } # not actually used by anything yet, but in the future say perl Build.PL --network
  80                            },
  81     auto_features       => {
  82                             BioDBSeqFeature_BDB   => {
  83                                                         description      => "BDB tests for Bio::DB::SeqFeature::Store",
  84                                                         feature_requires => { 'DB_File' => 0 } # feature_requires is like requires, execpt that it doesn't trigger installation
  85                                                      },
  86                             BioDBGFF              => {
  87                                                         description      => "BioDBGFF database tests (will need to answer questions before really enabling)",
  88                                                         feature_requires => { 'DBI' => 0 },
  89                                                         excludes_os      => ['mswin'],
  90                                                         test             => \&test_biodbgff # ModuleBuildBioperl unique requirement that after everything else succeeds, supplied code ref must also return undef
  91                                                      },
  92                             BioDBSeqFeature_mysql => {
  93                                                         description      => "MySQL tests for Bio::DB::SeqFeature::Store",
  94                                                         feature_requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
  95                                                         test             => \&test_db
  96                                                      },
  97 # The following code works, but since no tests in the test suite actually make use of this functionality, don't use it yet
  98 #                            Network               => {
  99 #                                                        description => "Enable tests that need an internet connection",
 100 #                                                        requires    => { 'LWP::UserAgent' => 0 },
 101 #                                                        options     => ['network'], # ModuleBuildBioperl unique requirement that --network was supplied
 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 # Handle auto features
 113 if ($build->feature('BioDBSeqFeature_BDB')) {
 114     make_bdb_test();
 115 }
 116 if ($build->feature('BioDBSeqFeature_mysql')) {
 117     make_dbi_test();
 118 }
 119 {
 120     $build->notes(network => $build->feature('Network'));
 121     # then in test script:
 122     #   use Module::Build;
 123     #   my $build = Module::Build->current;
 124     #   my $do_network_tests = $build->notes('network');
 125 }
 126
 127 # Ask questions
 128 $build->choose_scripts;
 129 prompt_for_biodbgff() if $build->feature('BioDBGFF');
 130
 131 # Request that some scripts run post-installation
 132 $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
 133
 134 # Add extra things to MANIFEST.SKIP
 135 $build->add_to_manifest_skip('bioperl.lisp', 'Bio/Tools/WebBlat.pm');
 136
 137 # Create the build script and exit
 138 $build->create_build_script;
 139
 140 exit;
 141
 142
 143 sub make_bdb_test {
 144     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 145     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_BDB.t');
 146     open my $F, ">$path";
 147     print $F <<END;
 148 system 'perl $path0 -adaptor berkeleydb -create 1 -temp 1';
 149 END
 150     close $F;
 151     $build->add_to_cleanup($path);
 152     $build->add_to_manifest_skip($path);
 153 }
 154
 155 sub test_db {
 156     eval {require DBI;};  # if not installed, this sub won't actually be called
 157     unless (eval {DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})}) {
 158         return "Could not connect to test database";
 159     }
 160     return;
 161 }
 162
 163 sub make_dbi_test {
 164     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 165     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_mysql.t');
 166     open my $F,">$path";
 167     print $F <<END;
 168 system 'perl $path0 -adaptor DBI::mysql -create 1 -temp 1 -dsn test';
 169 END
 170     close $F;
 171     $build->add_to_cleanup($path);
 172     $build->add_to_manifest_skip($path);
 173 }
 174
 175 sub test_biodbgff {
 176     eval {require DBI;};  # if not installed, this sub won't actually be called
 177     @drivers = DBI->available_drivers;
 178     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 179         return "MySQL, Pg nor Oracle DBI drivers are installed";
 180     }
 181     return;
 182 }
 183
 184 sub prompt_for_biodbgff {
 185     my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
 186
 187     if ($proceed) {
 188         my @driver_choices;
 189         foreach my $poss ('mysql', 'Pg', 'Oracle') {
 190             if (grep {/$poss/i} @drivers) {
 191                 my $choice = $poss;
 192                 $choice =~ s/^(.)/[$1]/;
 193                 push(@driver_choices, $choice);
 194             }
 195         }
 196
 197         my $driver;
 198         if (@driver_choices > 1) {
 199             my ($default) = $driver_choices[0] =~ /\[(.)/;
 200             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 201         }
 202         else {
 203             ($driver) = $driver_choices[0] =~ /\[(.)/;
 204         }
 205         if ($driver =~ /^[mM]/) {
 206             $driver = 'mysql';
 207         }
 208         elsif ($driver =~ /^[pP]/) {
 209             $driver = 'Pg';
 210         }
 211         elsif ($driver =~ /^[oO]/) {
 212             $driver = 'Oracle';
 213         }
 214
 215         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?", 'test');
 216         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 217         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 218         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 219
 220         my $use_host = 1;
 221         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 222             $use_host = 0;
 223         }
 224
 225         my $test_dsn;
 226         if ($driver eq 'Pg') {
 227             $test_dsn = "dbi:$driver:dbname=$test_db";
 228         }
 229         else {
 230             $test_dsn = "dbi:$driver:database=$test_db";
 231         }
 232         if ($use_host) {
 233             $test_dsn .= ";host=$test_host";
 234         }
 235
 236         $build->notes(dbd_driver => $driver);
 237         $build->notes(test_db => $test_db);
 238         $build->notes(test_host => $test_host);
 239         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 240         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 241         $build->notes(test_dsn => $test_dsn);
 242
 243         $build->log_info("  - will run the BioDBGFF tests with database driver '$driver' and these settings:\n",
 244                         "    Database $test_db\n",
 245                         "    Host     $test_host\n",
 246                         "    DSN      $test_dsn\n",
 247                         "    User     $test_user\n",
 248                         "    Password $test_pass\n");
 249     }
 250     else {
 251         $build->log_info("  - will not run the BioDBGFF live database tests\n");
 252     }
 253
 254     $build->log_info("\n");
 255 }