#!/usr/bin/perl # This is a Module::Build script for Bioperl installation. # See http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm # Uses a custom subclass of Module::Build called Bio::Root::Build # In the future developers may need to alter the requires and recommends # sections of Bio::Root::Build->new() below, but otherwise nothing else here is # likely to need changing. use strict; use lib '.'; use Bio::Root::Build; # XML::SAX::RTF doesn't work with BioPerl, at all, nada, zilch. # # Since we're running into this now on CPAN Testers, catch it up front and # deal with it. # # See: https://rt.cpan.org/Ticket/Display.html?id=5943 # https://redmine.open-bio.org/issues/2975 { eval { require XML::SAX; 1; }; unless ($@) { if (grep {$_->{Name} =~ 'XML::SAX::RTF'} @{XML::SAX->parsers()}) { warn < [0, # 'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'], 'Algorithm::Munkres' => [0, 'Phylogenetic Networks/Bio::PhyloNetwork'], 'Array::Compare' => [0, 'Phylogenetic Networks/Bio::PhyloNetwork'], 'YAML' => [0, 'GenBank->GFF3/bp_genbank2gff3.pl'], # this won't actually install due to circular dep, but we have no way of # doing a post-install the [circular dependency!] specifies it is only # installed on explicit request for this specific module, not when simply # choosing to install 'all' modules #'Bio::ASN1::EntrezGene' => [0, # 'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'], 'Clone' => [0, 'Cloning objects/Bio::Tools::Primer3'], 'Convert::Binary::C' => [0, 'Strider functionality/Bio::SeqIO::strider'], 'Error' => [0, 'OO-based exception handling (very optional)/Bio::Root::Exception'], 'GD' => [0, 'Alignment graphic output/Bio::Align::Graphics'], 'Graph' => [0, 'Phylogenetic Networks, ontology engine implementation, contig analysis'. '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'. 'Bio::Assembly::Tools::ContigSpectrum'], 'GraphViz' => [0, 'Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz'], 'HTML::Entities' => [0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml'], 'HTML::HeadParser' => [3, 'Parsing section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'], '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*'], 'List::MoreUtils' => [0, 'Back- or reverse-translation of sequences/'. 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'], 'LWP::UserAgent' => [0, 'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'], 'Math::Random' => [0, 'Random Phylogenetic Networks/Bio::PhyloNetwork::RandomFactory'], 'PostScript::TextBlock' => [0, 'EPS output/Bio::Tree::Draw::Cladogram'], 'Set::Scalar' => [0, 'Proper operation/Bio::Tree::Compatible'], 'SOAP::Lite' => [0, 'Bibliographic queries/Bio::DB::Biblio::soap'], 'Sort::Naturally' => [0, 'Sort lexically, but sort numeral parts numerically/'. 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'], 'Spreadsheet::ParseExcel' => [0, 'Parsing Excel files/Bio::SeqIO::excel'], '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'], 'SVG' => [2.26, 'Creating SVG images/Bio::Draw::Pictogram'], 'SVG::Graph' => [0.01, 'Creating SVG images/Bio::TreeIO::svggraph'], 'Text::ParseWords' => [0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'], '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'], 'XML::DOM::XPath' => [0.13, 'parsing interpro features/Bio::FeatureIO::interpro'], 'XML::Parser' => [0, 'parsing xml/Bio::Biblio::IO::medlinexml'], 'XML::Parser::PerlSAX' => [0, 'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,', 'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'], 'XML::SAX' => [0.15, 'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'], 'XML::SAX::Writer' => [0, 'Writing XML/Bio::SeqIO::tigrxml'], 'XML::Simple' => [0, 'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'], 'XML::Twig' => [0, 'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'. 'Bio::DB::Biblio::eutils'], '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'], ); my $mysql_ok = 0; my @drivers = available_drivers(); # Set up the Bio::Root::Build object my $build = Bio::Root::Build->new( module_name => 'Bio', dist_name => 'BioPerl', dist_version_from => 'Bio/Root/Version.pm', dist_author => 'BioPerl Team ', dist_abstract => 'Bioinformatics Toolkit', license => 'perl', no_index => {'dir' => [qw(examples/root/lib)]}, requires => { 'perl' => '5.6.1', 'IO::String' => 0, # why is this required? 'DB_File' => 0, # why is this required? 'Data::Stag' => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed 'Scalar::Util' => 0, # not in Perl 5.6.1, arrived in core in 5.7.3 'ExtUtils::Manifest' => '1.52', # allows spaces in file names }, build_requires => { 'Test::More' => 0, 'Module::Build' => 0.2805, 'Test::Harness' => 2.62, 'CPAN' => 1.81 }, recommends => { # reverted to a simple Module::Build-compatible hash, but we keep # additional data in the %recommends hash above. May be converted to # something simpler if there aren't complaints down the line. map {$_ => $recommends{$_}[0]} sort keys %recommends }, get_options => { accept => { }, network => { } # say 'perl Build.PL --network' to manually request network tests }, auto_features => { 'EntrezGene' => { description => "Presence of Bio::ASN1::EntrezGene", requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation }, 'DB_File Tests' => { description => "BDB tests for Bio::DB::SeqFeature::Store", requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation }, 'Bio::DB::GFF Tests' => { description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)", requires => { 'DBI' => 0 }, }, 'MySQL Tests' => { description => "MySQL-related tests for Bio::DB::SeqFeature::Store", requires => { 'DBI' => 0, 'DBD::mysql' => 0 }, }, 'Pg Tests' => { description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store", requires => { 'DBI' => 0, 'DBD::Pg' => 0}, }, 'SQLite Tests' => { description => "SQLite-related tests for Bio::DB::SeqFeature::Store", requires => { 'DBI' => 0, 'DBD::SQLite' => 0}, }, 'Network Tests' => { description => "Enable tests that need an internet connection", requires => { 'LWP::UserAgent' => 0 }, } }, dynamic_config => 1, #create_makefile_pl => 'passthrough', recursive_test_files => 1, # Extra files needed for BioPerl modules xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'}, #pm_files => {} # modules in Bio are treated as if they were in lib and auto-installed #script_files => [] # scripts in scripts directory are installed on-demand ); my $accept = $build->args('accept'); # how much do I hate this? Let me count the ways..... if (!$build->feature('EntrezGene')) { warn <feature('Bio::DB::GFF') || $build->feature('MySQL Tests') || $build->feature('MySQL Tests'); # Handle auto features if ($proceed && $build->feature('DB_File Tests')) { # will return without doing anything if user chose not to run tests during make_bdb_test(); } if ($proceed && ($build->feature('MySQL Tests') || $build->feature('Pg Tests') || $build->feature('SQLite Tests'))) { make_dbi_test(); } # Ask questions $build->choose_scripts($accept); if ($build->args('network')) { if ($build->feature('Network Tests')) { $build->notes(network => 1); $build->log_info(" - will run internet-requiring tests\n"); } else { $build->notes(network => 0); $build->log_info(" - Missing LWP::UserAgent, can't run network tests\n"); } } else { $build->prompt_for_network($accept) if $build->feature('Network Tests'); } # Add additional files here $build->add_build_element('xml'); # Create the build script and exit $build->create_build_script; exit; ########################## Helper subs ########################## sub make_bdb_test { my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t'); my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t'); unlink($path) if (-e $path); open(my $F, ">", $path) || die "Can't create test file\n"; print $F <add_to_cleanup($path); #$build->add_to_manifest_skip($path); } sub available_drivers { eval {require DBI; 1;}; # if not installed, this sub won't actually be called return if $@; @drivers = DBI->available_drivers; unless (grep {/mysql|Pg|SQLite/i} @drivers) { $mysql_ok = 0; return "Only MySQL, Postgres and SQLite DBI drivers supported for Bio::DB::SeqFeature RDMS tests"; } $mysql_ok = 1; return @drivers; } sub make_dbi_test { my $dsn = $build->notes('test_dsn') || return; my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t'); my $driver = $build->notes('dbd_driver'); my $path = File::Spec->catfile('t', 'LocalDB', ($driver eq 'mysql') ? 'SeqFeature_mysql.t' : ($driver eq 'SQLite') ? 'SeqFeature_SQLite.t' : 'SeqFeature_Pg.t'); my $test_db = $build->notes('test_db'); my $user = $build->notes('test_user'); my $pass = $build->notes('test_pass'); open my $F,">$path"; my $str = "$path0 -adaptor DBI::$driver -create 1 -temp 1 -dsn \"$dsn\""; $str .= " -user $user" if $user; $str .= " -password $pass" if $pass; print $F <add_to_cleanup($path); $build->add_to_cleanup($test_db) if $driver eq 'SQLite'; #$build->add_to_manifest_skip($path); } sub test_biodbgff { eval {require DBI;}; # if not installed, this sub won't actually be called return if $@; @drivers = DBI->available_drivers; unless (grep {/mysql|Pg|Oracle/i} @drivers) { return "MySQL, Pg nor Oracle DBI drivers are installed"; } return; } sub prompt_for_biodb { my $accept = shift; my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ". "Bio::DB::SeqFeature::Store live database tests? ". "y/n", 'n'); if ($proceed) { my @driver_choices; foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') { if (grep {/$poss/i} @drivers) { my $choice = $poss; $choice =~ s/^(.)/[$1]/; push(@driver_choices, $choice); } } my $driver; if (@driver_choices > 1) { my ($default) = $driver_choices[0] =~ /\[(.)/; $driver = $build->prompt("Which database driver should be used? ".join(" ", @driver_choices), $default); } else { ($driver) = $driver_choices[0] =~ /\[(.)/; } if ($driver =~ /^[mM]/) { $driver = 'mysql'; } elsif ($driver =~ /^[pP]/) { $driver = 'Pg'; } elsif ($driver =~ /^[oO]/) { $driver = 'Oracle'; } elsif ($driver =~ /^[sS]/) { $driver = 'SQLite'; } my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n". "This database should already be present but doesn't have to ". "be preloaded for any schema", 'test'); my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost'); my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef'); my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef'); my $use_host = 1; if ($test_host eq 'undef' || $test_host eq 'localhost') { $use_host = 0; } my $test_dsn; if ($driver eq 'Pg' || $driver eq 'SQLite') { $test_dsn = "dbi:$driver:dbname=$test_db"; $mysql_ok = 0; } else { $test_dsn = "dbi:$driver:database=$test_db"; $mysql_ok = 0; } if ($use_host) { $test_dsn .= ";host=$test_host"; } $build->notes(dbd_driver => $driver); $build->notes(test_db => $test_db); $build->notes(test_host => $test_host); $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user); $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass); $build->notes(test_dsn => $test_dsn); $build->log_info(" - will run tests with database driver '$driver' and these settings:\n", " Database $test_db\n", " Host $test_host\n", " DSN $test_dsn\n", " User $test_user\n", " Password $test_pass\n"); $build->log_info(" - will not run the BioDBSeqFeature live ". "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg'); } else { $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); } $build->log_info("\n"); return $proceed; }