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Build.PL
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#!/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 <<WARN;
############################# WARNING #############################
XML::SAX::RTF is not XML::SAX-compliant but is registered as an
XML::SAX parser. If used as the primary parser, modules requiring
XML::SAX will NOT work. Please install another XML::SAX-compliant
module and modify your local ParserDetails.ini file per XML::SAX
docs to remove references to XML::SAX::RTF.
############################# WARNING #############################
WARN
sleep 2;
}
}
}
my %recommends = (
# AcePerl support is deprecated, per LDS - cjfields - 5-5-2011
#'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!]'],
'Clone' => [0,
'Cloning objects/Bio::Root::Root,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' => [0.50,
'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 <HEAD> 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*'],
'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'],
'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,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::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'],
'YAML' => [0,
'GenBank->GFF3/bp_genbank2gff3.pl'],
);
my $mysql_ok = 0;
my @drivers = available_drivers();
# Set up the Bio::Root::Build object
my $build = Bio::Root::Build->new(
module_name => 'Bio',
dist_name => 'BioPerl',
dist_version => '1.006924',
dist_author => 'BioPerl Team <[email protected]>',
dist_abstract => 'Bioinformatics Toolkit',
license => 'perl',
no_index => {'x_dir' => [qw(examples/root/lib)]},
requires => {
'perl' => '5.6.1',
'IO::String' => 0, # why is this required?
'DB_File' => 0, # why is this required?
'Data::Stag' => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
'Scalar::Util' => 0, # not in Perl 5.6.1, arrived in core in 5.7.3
'ExtUtils::Manifest' => '1.52', # allows spaces in file names
},
build_requires => {
'CPAN' => 1.81,
'Module::Build' => 0.2805,
'Test::Harness' => 2.62,
'Test::Most' => 0,
'URI::Escape' => 0
},
recommends => {
# reverted to a simple Module::Build-compatible hash, but we keep
# additional data in the %recommends hash above. May be converted to
# something simpler if there aren't complaints down the line.
map {$_ => $recommends{$_}[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,
#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 <<WARN;
############################## WARNING #############################
#
#Bio::ASN1::EntrezGene not found. This is an *optional* module;
#however, because it has a circular dependency with BioPerl we do not
#include it on our list of recommended modules.
#
#If you require EntrezGene functionality, you can install
#Bio::ASN1::EntrezGene after BioPerl has finished installing.
#
############################## WARNING #############################
#
#WARN
# sleep 3;
#}
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');
# 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 $F <<END;
system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
END
close $F;
$build->add_to_cleanup($path);
#$build->add_to_manifest_skip($path);
}
sub 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 $F <<END;
system '$^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
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;
}