#!/usr/bin/perl -w # 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; our @drivers; my $mysql_ok = 0; # 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', requires => { 'perl' => '5.6.1', 'IO::String' => 0, 'DB_File' => 0, '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 => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml 'Ace' => '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!]', # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0 'Clone' => '0/cloning objects/Bio::Tools::Primer3', 'Convert::Binary::C' => '0/strider functionality/Bio::SeqIO::strider', # we specifically want Graph::Directed, but that has no VERSION 'Graph' => '0/ontology engine implementation for the GO parser/Bio::PhyloNetwork', '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', 'Spreadsheet::ParseExcel' => '0/parsing Excel files/Bio::SeqIO::excel,Bio::Microarray::Tools::ReseqChip', 'Spreadsheet::WriteExcel' => '0/writing Excel files/Bio::Microarray::Tools::ReseqChip', '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', }, get_options => { accept => { }, network => { } # say 'perl Build.PL --network' to manually request network tests }, auto_features => { BioDBSeqFeature_BDB => { description => "BDB tests for Bio::DB::SeqFeature::Store", feature_requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation }, BioDBGFF => { description => "BioDBGFF database tests (will need to answer questions before really enabling)", feature_requires => { 'DBI' => 0 }, excludes_os => ['mswin'], test => \&test_biodbgff # Bio::Root::Build unique requirement that after everything else succeeds, supplied code ref must also return undef }, BioDBSeqFeature_mysql => { description => "MySQL tests for Bio::DB::SeqFeature::Store", feature_requires => { 'DBI' => 0, 'DBD::mysql' => 0 }, test => \&test_db_sf }, BioDBSeqFeature_Pg => { description => "Postgres tests for Bio::DB::SeqFeature::Store", feature_requires => { 'DBI' => 0, 'DBD::Pg' => 0}, test => \&test_db_sf }, BioDBSeqFeature_SQLite => { description => "SQLite tests for Bio::DB::SeqFeature::Store", feature_requires => { 'DBI' => 0, 'DBD::SQLite' => 0}, test => \&test_db_sf }, Network => { description => "Enable tests that need an internet connection", feature_requires => { 'LWP::UserAgent' => 0 }, test => \&Bio::Root::Build::test_internet } }, 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}; my $proceed = prompt_for_biodb($accept) if $build->feature('BioDBGFF') || $build->feature('BioDBSeqFeature_mysql'); # Handle auto features if ($proceed && $build->feature('BioDBSeqFeature_BDB')) { # will return without doing anything if user chose not to run tests during # prompt_for_biodb() above make_bdb_test(); } if ($proceed && ($build->feature('BioDBSeqFeature_mysql') or $build->feature('BioDBSeqFeature_Pg'))) { make_dbi_test(); } # Ask questions $build->choose_scripts($accept); #prompt_for_biodbgff($accept) if $build->feature('BioDBGFF'); { if ($build->args('network')) { if ($build->feature('Network')) { $build->notes(network => 1); $build->log_info(" - will run internet-requiring tests\n"); } else { $build->notes(network => 0); $build->log_info(" - will not run network tests since I seem to be missing essential network functionality\n"); } } else { $build->prompt_for_network($accept) if $build->feature('Network'); } # then in test script: # use Bio::Root::Build; # my $build = Module::Build->current; # my $do_network_tests = $build->notes('network'); } # Request that some scripts run post-installation $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS # Add extra things to MANIFEST.SKIP $build->add_to_manifest_skip('bioperl.lisp'); # Add additional files here $build->add_build_element('xml'); # Create the build script and exit $build->create_build_script; exit; 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 test_db_sf { eval {require DBI;}; # if not installed, this sub won't actually be called @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; } 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 @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; }