[med-svn] r331 - trunk/packages/bioperl/trunk
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Fri Jun 15 02:37:21 UTC 2007
Author: charles-guest
Date: 2007-06-15 02:37:21 +0000 (Fri, 15 Jun 2007)
New Revision: 331
Removed:
trunk/packages/bioperl/trunk/Build.PL
Log:
using quilt instead of diff.gz
Deleted: trunk/packages/bioperl/trunk/Build.PL
===================================================================
--- trunk/packages/bioperl/trunk/Build.PL 2007-06-15 02:36:12 UTC (rev 330)
+++ trunk/packages/bioperl/trunk/Build.PL 2007-06-15 02:37:21 UTC (rev 331)
@@ -1,257 +0,0 @@
-#!/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 ModuleBuildBioperl that
-# doesn't get installed
-
-# In the future developers may need to alter the requires and recommends and
-# possibly Network sections of ModuleBuildBioperl->new() below, but otherwise
-# nothing else here is likely to need changing.
-
-use strict;
-use ModuleBuildBioperl;
-
-our @drivers;
-
-# Set up the ModuleBuildBioperl object
-my $build = ModuleBuildBioperl->new(
- module_name => 'Bio',
- dist_name => 'bioperl',
- dist_version_from => 'Bio/Root/Version.pm',
- dist_author => 'Bioperl Team <bioperl-l at bioperl.org>',
- dist_abstract => 'Bioinformatics Toolkit',
- license => 'artistic',
- requires => {
- 'perl' => '5.6.1',
- 'IO::String' => 0,
- 'DB_File' => 0
- },
- 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',
- # this won't actually install due to circular dep, but we have no way of doing a post-install
- 'Bio::ASN1::EntrezGene' => '0/parsing entrezgene/Bio::SeqIO::entrezgene',
- # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
- 'Class::AutoClass' => '1/creating objects/Bio::Graph::SimpleGraph,Bio::Graph::SimpleGraph::Traversal,Bio::Graph::ProteinGraph',
- 'Clone' => '0/cloning objects/Bio::Graph::ProteinGraph,Bio::Tools::Primer3',
- 'Convert::Binary::C' => '0/strider functionality/Bio::SeqIO::strider',
- 'Data::Stag::XMLWriter' => '0/writing choas xml files/Bio::SeqIO::chaosxml',
- 'GD' => '1.3/rendering Sequences and Features/Bio::Graphics::Glyph*',
- 'GD::SVG' => '0/creating SVG images/Bio::Graphics::Panel',
- # we specifically want Graph::Directed, but that has no VERSION
- 'Graph' => '0/ontology engine implementation for the GO parser/Bio::Ontology::SimpleGOEngine::GraphAdaptor',
- 'HTML::Entities' => '0/remote analysis POST submissions/Bio::SearchIO::blastxml',
- 'HTML::Parser' => '3/screen scraping www.gdb.org/Bio::DB::GDB',
- '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*',
- 'LWP::UserAgent' => '0/remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::Tools::WebBlat,Bio::WebAgent,Bio::Graphics::Glyph::image',
- 'PostScript::TextBlock' => '0/EPS output/Bio::Tree::Draw::Cladogram',
- 'Set::Scalar' => '0/proper operation/Bio::Tree::Compatible',
- 'SOAP::Lite' => '0/XEMBL Services and Bibliographic queries/Bio::DB::XEMBLService,Bio::DB::Biblio::soap',
- 'Spreadsheet::ParseExcel' => '0/parsing Excel files/Bio::SeqIO::excel',
- 'Storable' => '0/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/SVG output/Bio::Graphics::Pictogram',
- 'SVG::Graph' => '0.01/creating SVG images/Bio::TreeIO::svggraph',
- 'Text::Shellwords' => '0/test scripts/Bio::Graphics',
- 'URI::Escape' => '0/dealing with web resources/Bio::Tools::WebBlat,Bio::FeatureIO::gff,Bio::FeatureIO::interpro,Bio::DB::Biblio::eutils,Bio::DB::EUtilities::Cookie,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::Twig' => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils,Bio::Graph::IO::psi_xml',
- '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 => {
- network => { } # not actually used by anything yet, but in the future say perl Build.PL --network
- },
- auto_features => {
- BioDBSeqFeature_BDB => {
- description => "BDB tests for Bio::DB::SeqFeature::Store",
- feature_requires => { 'DB_File' => 0 } # feature_requires is like requires, execpt 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 # ModuleBuildBioperl 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
- },
-# The following code works, but since no tests in the test suite actually make use of this functionality, don't use it yet
-# Network => {
-# description => "Enable tests that need an internet connection",
-# requires => { 'LWP::UserAgent' => 0 },
-# options => ['network'], # ModuleBuildBioperl unique requirement that --network was supplied
-# test => \&ModuleBuildBioperl::test_internet
-# }
- },
- dynamic_config => 1
-
- #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
-);
-
-# Handle auto features
-if ($build->feature('BioDBSeqFeature_BDB')) {
- make_bdb_test();
-}
-if ($build->feature('BioDBSeqFeature_mysql')) {
- make_dbi_test();
-}
-{
- $build->notes(network => $build->feature('Network'));
- # then in test script:
- # use Module::Build;
- # my $build = Module::Build->current;
- # my $do_network_tests = $build->notes('network');
-}
-
-# Ask questions
-$build->choose_scripts;
-prompt_for_biodbgff() if $build->feature('BioDBGFF');
-
-# Request that some scripts run post-installation
-$build->add_post_install_script('maintenance/symlink_script.pl'); # takes a unix file path regardless of local OS
-
-# Add extra things to MANIFEST.SKIP
-$build->add_to_manifest_skip('bioperl.lisp', 'Bio/Tools/WebBlat.pm');
-
-# Create the build script and exit
-$build->create_build_script;
-
-exit;
-
-
-sub make_bdb_test {
- my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
- my $path = File::Spec->catfile('t', 'BioDBSeqFeature_BDB.t');
- open my $F, ">$path";
- print $F <<END;
-system 'perl $path0 -adaptor berkeleydb -create 1 -temp 1';
-END
- close $F;
- $build->add_to_cleanup($path);
- $build->add_to_manifest_skip($path);
-}
-
-sub test_db {
- eval {require DBI;}; # if not installed, this sub won't actually be called
- unless (eval {DBI->connect('dbi:mysql:test',undef,undef,{RaiseError=>0,PrintError=>0})}) {
- return "Could not connect to test database";
- }
- return;
-}
-
-sub make_dbi_test {
- my $path0 = File::Spec->catfile('t', 'BioDBSeqFeature.t');
- my $path = File::Spec->catfile('t', 'BioDBSeqFeature_mysql.t');
- open my $F,">$path";
- print $F <<END;
-system 'perl $path0 -adaptor DBI::mysql -create 1 -temp 1 -dsn test';
-END
- close $F;
- $build->add_to_cleanup($path);
- $build->add_to_manifest_skip($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_biodbgff {
- my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n');
-
- if ($proceed) {
- my @driver_choices;
- foreach my $poss ('mysql', 'Pg', 'Oracle') {
- if (grep {/$poss/i} @drivers) {
- my $choice = $poss;
- $choice =~ s/^(.)/[$1]/;
- push(@driver_choices, $choice);
- }
- }
-
- my $cfg = {};
-
- 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';
- }
- $cfg->{dbd_driver} = $driver;
-
- $cfg->{test_db} = $build->prompt("Which database should I use for testing the $driver driver?", 'test');
- $cfg->{test_host} = $build->prompt("On which host is database $cfg->{test_db} running (hostname, ip address or host:port)", 'localhost');
- my $test_user = $build->prompt("User name for connecting to database $cfg->{test_db}?", 'undef');
- $cfg->{test_user} = $test_user eq 'undef' ? '' : $test_user;
- my $test_pass = $build->prompt("Password for connecting to database $cfg->{test_db}?", 'undef');
- $cfg->{test_pass} = $test_pass eq 'undef' ? '' : $test_pass;
-
- my $use_host = 1;
- if ($cfg->{test_host} eq 'undef' || $cfg->{test_host} eq 'localhost') {
- $use_host = 0;
- }
-
- my $test_dsn;
- if ($driver eq 'Pg') {
- $test_dsn = "dbi:$driver:dbname=$cfg->{test_db}";
- }
- else {
- $test_dsn = "dbi:$driver:database=$cfg->{test_db}";
- }
- if ($use_host) {
- $test_dsn .= ";host=$cfg->{test_host}";
- }
- $cfg->{test_dsn} = $test_dsn;
-
- my $path = File::Spec->catfile('t', 'do_biodbgff.tests');
- if (open T,">$path") {
- while (my ($key, $value) = each %$cfg) {
- print T $key, "\t", $value,"\n";
- }
- close T;
- }
-
- $build->add_to_cleanup($path);
- $build->add_to_manifest_skip($path);
-
- $build->log_info(" - will run the BioDBGFF tests with database driver '$driver' and these settings:\n",
- " Database $cfg->{test_db}\n",
- " Host $cfg->{test_host}\n",
- " DSN $test_dsn\n",
- " User $test_user\n",
- " Password $test_pass\n");
- }
- else {
- $build->log_info(" - will not run the BioDBGFF live database tests\n");
- }
-
- $build->log_info("\n");
-}
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