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#!/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 <bioperl-l@bioperl.org>',
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 <HEAD> 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 $F <<END;
system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
END
close $F;
$build->add_to_cleanup($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 $F <<END;
system '$^X $str';
END
close $F;
$build->add_to_cleanup($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;
}
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