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::Shellwords'          => '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 prompt_for_biodb() if $build->feature('BioDBGFF') || $build->feature('BioDBSeqFeature_mysql');
 113
 114 # Handle auto features
 115 if ($build->feature('BioDBSeqFeature_BDB')) {
 116     make_bdb_test();
 117 }
 118 if ($build->feature('BioDBSeqFeature_mysql') && $mysql_ok) {
 119     # will return without doing anything if user chose not to run tests during
 120     # prompt_for_biodb() above
 121     make_dbi_test();
 122 }
 123
 124 # Ask questions
 125 $build->choose_scripts;
 126 {
 127     if ($build->args('network')) {
 128         if ($build->feature('Network')) {
 129             $build->notes(network => 1);
 130             $build->log_info("  - will run internet-requiring tests\n");
 131         }
 132         else {
 133             $build->notes(network => 0);
 134             $build->log_info("  - will not run network tests since I seem to be missing essential network functionality\n");
 135         }
 136     }
 137     else {
 138         prompt_for_network() if $build->feature('Network');
 139     }
 140     # then in test script:
 141     #   use Module::Build;
 142     #   my $build = Module::Build->current;
 143     #   my $do_network_tests = $build->notes('network');
 144 }
 145
 146 # Request that some scripts run post-installation
 147 $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
 148
 149 # Add extra things to MANIFEST.SKIP
 150 $build->add_to_manifest_skip('bioperl.lisp', 'Bio/Tools/WebBlat.pm');
 151
 152 # Create the build script and exit
 153 $build->create_build_script;
 154
 155 exit;
 156
 157 sub make_bdb_test {
 158     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 159     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_BDB.t');
 160     unlink($path) if (-e $path);
 161     open(my $F, ">", $path) || die "Can't create test file\n";
 162     print $F <<END;
 163 system 'perl $path0 -adaptor berkeleydb -create 1 -temp 1';
 164 END
 165     close $F;
 166     $build->add_to_cleanup($path);
 167     $build->add_to_manifest_skip($path);
 168 }
 169
 170 sub test_db_sf {
 171     eval {require DBI;};  # if not installed, this sub won't actually be called
 172     @drivers = DBI->available_drivers;
 173     unless (grep {/mysql/i} @drivers) {
 174         $mysql_ok = 0;
 175         return "Only MySQL DBI driver supported for BioDBSeqFeature_mysql tests";
 176     }
 177     $mysql_ok = 1;
 178     return;
 179 }
 180
 181 sub make_dbi_test {
 182     my $dsn = $build->notes('test_dsn') || return;
 183     my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
 184     my $path = File::Spec->catfile('t', 'BioDBSeqFeature_mysql.t');
 185     my $test_db = $build->notes('test_db');
 186     my $user = $build->notes('test_user');
 187     my $pass = $build->notes('test_pass');
 188     open my $F,">$path";
 189     my $str = "$path0 -adaptor DBI::mysql -create 1 -temp 1 -dsn $dsn";
 190     $str .= " -user $user" if $user;
 191     $str .= " -password $pass" if $pass;
 192     print $F <<END;
 193     system 'perl $str';
 194 END
 195     close $F;
 196     $build->add_to_cleanup($path);
 197     $build->add_to_manifest_skip($path);
 198 }
 199
 200 sub test_biodbgff {
 201     eval {require DBI;};  # if not installed, this sub won't actually be called
 202     @drivers = DBI->available_drivers;
 203     unless (grep {/mysql|Pg|Oracle/i} @drivers) {
 204         return "MySQL, Pg nor Oracle DBI drivers are installed";
 205     }
 206     return;
 207 }
 208
 209 sub prompt_for_biodb {
 210     my $proceed = $build->y_n("Do you want to run the BioDBGFF or ".
 211                               "BioDBSeqFeature_mysql live database tests? ".
 212                               "y/n", 'n');
 213
 214     if ($proceed) {
 215         my @driver_choices;
 216         foreach my $poss ('mysql', 'Pg', 'Oracle') {
 217             if (grep {/$poss/i} @drivers) {
 218                 my $choice = $poss;
 219                 $choice =~ s/^(.)/[$1]/;
 220                 push(@driver_choices, $choice);
 221             }
 222         }
 223
 224         my $driver;
 225         if (@driver_choices > 1) {
 226             my ($default) = $driver_choices[0] =~ /\[(.)/;
 227             $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default);
 228         }
 229         else {
 230             ($driver) = $driver_choices[0] =~ /\[(.)/;
 231         }
 232         if ($driver =~ /^[mM]/) {
 233             $driver = 'mysql';
 234         }
 235         elsif ($driver =~ /^[pP]/) {
 236             $mysql_ok = 0;
 237             $driver = 'Pg';
 238         }
 239         elsif ($driver =~ /^[oO]/) {
 240             $mysql_ok = 0;
 241             $driver = 'Oracle';
 242         }
 243
 244         my $test_db = $build->prompt("Which database should I use for testing the $driver driver?", 'test');
 245         my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
 246         my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
 247         my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');
 248
 249         my $use_host = 1;
 250         if ($test_host eq 'undef' || $test_host eq 'localhost') {
 251             $use_host = 0;
 252         }
 253
 254         my $test_dsn;
 255         if ($driver eq 'Pg') {
 256             $test_dsn = "dbi:$driver:dbname=$test_db";
 257         }
 258         else {
 259             $test_dsn = "dbi:$driver:database=$test_db";
 260         }
 261         if ($use_host) {
 262             $test_dsn .= ";host=$test_host";
 263         }
 264
 265         $build->notes(dbd_driver => $driver);
 266         $build->notes(test_db => $test_db);
 267         $build->notes(test_host => $test_host);
 268         $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
 269         $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
 270         $build->notes(test_dsn => $test_dsn);
 271
 272         $build->log_info("  - will run tests with database driver '$driver' and these settings:\n",
 273                         "    Database $test_db\n",
 274                         "    Host     $test_host\n",
 275                         "    DSN      $test_dsn\n",
 276                         "    User     $test_user\n",
 277                         "    Password $test_pass\n");
 278         $build->log_info("  - will not run the BioDBSeqFeature_mysql live ".
 279                          "database tests (requires MySQL driver)\n") unless $mysql_ok;
 280     }
 281     else {
 282         $build->log_info("  - will not run the BioDBGFF live database tests\n");
 283     }
 284
 285     $build->log_info("\n");
 286 }
 287
 288 sub prompt_for_network {
 289     my $proceed = $build->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
 290
 291     if ($proceed) {
 292         $build->notes(network => 1);
 293         $build->log_info("  - will run internet-requiring tests\n");
 294     }
 295     else {
 296         $build->notes(network => 0);
 297         $build->log_info("  - will not run internet-requiring tests\n");
 298     }
 299 }