#!/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' ], # 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!]'], 'Bio::Phylo' => [ 0, 'NeXML related modules/Bio::AlignIO::nexml,Bio::Nexml::Factory,' . 'Bio::SeqIO::nexml,Bio::TreeIO::nexml' ], 'CGI' => [ 0, 'CGI-y things/Bio::DB::Query::HIVQuery' ], 'Clone' => [ 0, 'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3' ], 'Convert::Binary::C' => [ 0, 'Strider functionality/Bio::SeqIO::strider' ], 'DB_File' => [ 0, 'Database functionality/Bio::Assemby,Bio::DB' ], 'Error' => [ 0, 'OO-based exception handling (very optional)/Bio::Root::Exception' ], 'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ], 'Graph' => [ 0.50, 'Phylogenetic Networks, ontology engine implementation, contig analysis' . '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,' . 'Bio::Assembly::Tools::ContigSpectrum' ], 'GraphViz' => [ 0, 'Phylogenetic Network Visualization/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' ], 'HTML::TableExtract' => [ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ], '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*' ], 'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ], 'IO::Scalar' => [ 0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat' ], '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' ], 'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ], 'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ], '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,Bio::Root::Root' ], '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' ], 'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ], 'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ], 'XML::LibXML' => [ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ], 'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ], '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' ], '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' ], 'YAML' => [ 0, 'GenBank->GFF3/bp_genbank2gff3.pl' ], ); 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 => $Bio::Root::Version::VERSION, dist_author => 'BioPerl Team ', dist_abstract => 'Bioinformatics Toolkit', license => 'perl', requires => { 'perl' => '5.6.1', 'IO::String' => 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 }, configure_requires => { 'Module::Build' => 0.42, }, build_requires => { 'Module::Build' => 0.42, 'CPAN' => 1.81, 'Test::Harness' => 2.62, 'Test::Most' => 0, 'URI::Escape' => 0 }, 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, 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'); my $proceed = prompt_for_biodb($accept) if $build->feature('Bio::DB::GFF') || $build->feature('MySQL Tests') || $build->feature('Pg Tests') || $build->feature('SQLite 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'); if ( ! -e 'MANIFEST' ) { $build->ACTION_manifest(); } # 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, '>', $path or die "Could not write test file '$path': $!\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, '>', $path or die "Could not write file '$path' for DBI test: $!\n"; 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; }