Build.PL

   1 use Module::Build;
   2 my $class = Module::Build->subclass(
   3     class => 'Module::Build::SGNSite',
   4     code  => <<'SUBCLASS',
   5
   6 # build action just runs make on programs
   7 sub ACTION_build {
   8    my $self = shift;
   9    $self->SUPER::ACTION_build(@_);
  10    system "make -C programs";
  11    $? and die "make failed\n";
  12 }
  13
  14 # override install to just copy the whole dir into the install_base
  15 sub ACTION_install {
  16    my $self = shift;
  17    $self->SUPER::ACTION_install(@_);
  18
  19    my @install_dirs = qw|cgi-bin conf documents mason programs support_data t features js |;
  20
  21    require File::Spec;
  22    my $tgt_dir = File::Spec->catdir($self->install_base,'sgn');
  23    mkdir $tgt_dir;
  24    system 'cp', '-rl', @install_dirs => $tgt_dir;
  25    $? and die "SGN site copy failed\n";
  26 }
  27
  28 sub ACTION_clean {
  29    shift->SUPER::ACTION_clean(@_);
  30    system "make -C programs clean";
  31    $? and die "SGN site copy failed\n";
  32 }
  33 SUBCLASS
  34 );
  35
  36 #my $class = 'Module::Build';
  37 my $build = $class->new(
  38
  39     dist_name          => 'SGN',
  40     license            => 'perl',
  41     create_makefile_pl => 'passthrough',
  42
  43     module_name        => 'SGN::Context',
  44
  45     # current version of our core libraries distribution
  46     dist_version => '0.1',
  47     dist_author  => 'Lukas Mueller',
  48     dist_abstract =>
  49 'The code and content behind the Sol Genomics Network main website, http://solgenomics.net',
  50
  51     recursive_test_files => 1,
  52
  53     build_requires => {
  54         'Class::MethodMaker' => 0,
  55
  56         #         'CXGN::DB::Connection' => 0,
  57         #         'CXGN::Genomic::Clone' => 0,
  58         #         'CXGN::Page' => 0,
  59         #         'CXGN::People::Person' => 0,
  60         #         'CXGN::VHost::Test' => 0,
  61         'File::Temp'           => 0,
  62         'HTML::Lint'           => 0,
  63         'JSON'                 => 0,
  64         'List::Util'           => 0,
  65         'Test::More'           => 0,
  66         'Test::Most'           => 0,
  67         'Test::WWW::Mechanize' => 0,
  68         'Test::WWW::Selenium'  => 0,
  69         'Test::MockObject'     => 0,
  70     },
  71     requires => {
  72         'perl'                => '5.10.0',
  73         'autodie'             => 0,
  74         'IPC::System::Simple' => 0,         #< required for autodie :all
  75         'Apache::DBI'         => 0,
  76
  77         #        'Apache2::Request' => 0,
  78         'Bio::Chado::Schema' => '0.05900',
  79
  80         'Bio::Root::Version'     => '1.006001',
  81         #         'Bio::AlignIO' => 0,
  82         #         'Bio::DB::GenBank' => 0,
  83         #         'Bio::GMOD::Blast::Graph' => 0,
  84         #         'Bio::Range' => 0,
  85         #         'Bio::Restriction::Analysis' => 0,
  86         #         'Bio::SearchIO' => 0,
  87         #         'Bio::Seq' => 0,
  88         #         'Bio::SeqIO' => 0,
  89         #         'Bio::Tools::Primer3' => 0,
  90         #         'Bio::Tools::Run::Primer3' => 0,
  91         #         'Bio::Graphics::Gel' => 0,
  92
  93         'Bio::Graphics::FeatureFile' => 0,
  94
  95         'Cache::File' => 0,
  96
  97
  98         'Catalyst::Runtime'                => '5.80024',
  99         'Catalyst::Controller::CGIBin'     => '0.029',
 100         'Catalyst::Action::RenderView'     => 0,
 101         'Catalyst::Plugin::ErrorCatcher'   => 0,
 102         'Catalyst::Plugin::ErrorCatcher::Email'
 103                                            => 0,
 104         'Catalyst::Plugin::StackTrace'     => 0,
 105         'Catalyst::Plugin::Static::Simple' => 0,
 106         'Catalyst::View::HTML::Mason'      => 0,
 107         'Catalyst::View::JavaScript::Minifier::XS'
 108                                            => '2.100000',
 109         'CatalystX::GlobalContext'         => 0,
 110
 111         'CGI'                              => 0,
 112         'CGI::Carp::DebugScreen'           => '0.16',
 113
 114         #         'CXGN::Accession' => 0,
 115         #         'CXGN::Accession::Tools' => 0,
 116         #         'CXGN::Alignment' => 0,
 117         #         'CXGN::Apache::Error' => 0,
 118         #         'CXGN::Apache::Request' => 0,
 119         #         'CXGN::BioTools::AGP' => 0,
 120         #         'CXGN::BioTools::CapsDesigner2' => 0,
 121         #         'CXGN::BioTools::SearchIOHTMLWriter' => 0,
 122         #         'CXGN::BlastDB' => 0,
 123         #         'CXGN::BlastWatch' => 0,
 124         #         'CXGN::Bulk' => 0,
 125         #         'CXGN::CDBI::Auto::SGN::Organism' => 0,
 126         #         'CXGN::CDBI::Auto::SGNSubmit::Facility' => 0,
 127         #         'CXGN::CDBI::Auto::SGNSubmit::Library' => 0,
 128         #         'CXGN::Chado::CV' => 0,
 129         #         'CXGN::Chado::Cvterm' => 0,
 130         #         'CXGN::Chado::Dbxref' => 0,
 131         #         'CXGN::Chado::Feature' => 0,
 132         #         'CXGN::Chado::Ontology' => 0,
 133         #         'CXGN::Chado::Organism' => 0,
 134         #         'CXGN::Chado::Phenotype' => 0,
 135         #         'CXGN::Chado::Pubauthor' => 0,
 136         #         'CXGN::Chado::Publication' => 0,
 137         #         'CXGN::Chromatogram' => 0,
 138         #         'CXGN::Contact' => 0,
 139         #         'CXGN::Cookie' => 0,
 140         #         'CXGN::Cview' => 0,
 141         #         'CXGN::Cview::ChrLink' => 0,
 142         #         'CXGN::Cview::ChrMarkerImage' => 0,
 143         #         'CXGN::Cview::Chromosome::Vector' => 0,
 144         #         'CXGN::Cview::ChromosomeViewer' => 0,
 145         #         'CXGN::Cview::Map::SGN::User' => 0,
 146         #         'CXGN::Cview::Map::Tools' => 0,
 147         #         'CXGN::Cview::Map_overviews' => 0,
 148         #         'CXGN::Cview::Map_overviews::Generic' => 0,
 149         #         'CXGN::Cview::Map_overviews::ProjectStats' => 0,
 150         #         'CXGN::Cview::MapFactory' => 0,
 151         #         'CXGN::Cview::MapImage' => 0,
 152         #         'CXGN::Cview::Marker::RangeMarker' => 0,
 153         #         'CXGN::Cview::Marker::VectorFeature' => 0,
 154         #         'CXGN::Cview::Utils' => 0,
 155         #         'CXGN::Cview::VectorViewer' => 0,
 156         #         'CXGN::Cvterms' => 0,
 157         #         'CXGN::DB::Connection' => 0,
 158         #         'CXGN::DB::ModifiableI' => 0,
 159         #         'CXGN::DB::Object' => 0,
 160         #         'CXGN::DB::PhenoPopulation' => 0,
 161         #         'CXGN::DB::Physical' => 0,
 162         #         'CXGN::Debug' => 0,
 163         #         'CXGN::Feed' => 0,
 164         #         'CXGN::Fish' => 0,
 165         #         'CXGN::Garbage::Sequence' => 0,
 166         #         'CXGN::Genomic' => 0,
 167         #         'CXGN::Genomic::Chromat' => 0,
 168         #         'CXGN::Genomic::Clone' => 0,
 169         #         'CXGN::Genomic::CloneIdentifiers' => 0,
 170         #         'CXGN::Genomic::CloneNameParser' => 0,
 171         #         'CXGN::Genomic::GSS' => 0,
 172         #         'CXGN::Genomic::Library' => 0,
 173         #         'CXGN::Genomic::Search::Clone' => 0,
 174         #         'CXGN::Genomic::Tools' => 0,
 175         #         'CXGN::Glossary' => 0,
 176         #         'CXGN::Graphics::BlastGraph' => 0,
 177         #         'CXGN::Image' => 0,
 178         #         'CXGN::Image::GDImage' => 0,
 179         #         'CXGN::Insitu' => 0,
 180         #         'CXGN::Insitu::DB' => 0,
 181         #         'CXGN::Insitu::Experiment' => 0,
 182         #         'CXGN::Insitu::ExperimentSearch' => 0,
 183         #         'CXGN::Insitu::Image' => 0,
 184         #         'CXGN::Insitu::Organism' => 0,
 185         #         'CXGN::Insitu::Primer' => 0,
 186         #         'CXGN::Insitu::Probe' => 0,
 187         #         'CXGN::Insitu::Tag' => 0,
 188         #         'CXGN::Insitu::Toolbar' => 0,
 189         #         'CXGN::ITAG::Pipeline' => 0,
 190         #         'CXGN::ITAG::Release' => 0,
 191         #         'CXGN::Login' => 0,
 192         #         'CXGN::Map' => 0,
 193         #         'CXGN::Map::Tools' => 0,
 194         #         'CXGN::Marker' => 0,
 195         #         'CXGN::Marker::Search' => 0,
 196         #         'CXGN::Marker::SNP::Schema' => 0,
 197         #         'CXGN::Marker::SNP::Snp' => 0,
 198         #         'CXGN::Marker::Tools' => 0,
 199         #         'CXGN::Metadata' => 0,
 200         #         'CXGN::MOBY::LocalServices' => 0,
 201         #         'CXGN::Page' => 0,
 202         #         'CXGN::Page::Form::EditableCheckbox' => 0,
 203         #         'CXGN::Page::Form::SimpleFormPage' => 0,
 204         #         'CXGN::Page::FormattingHelpers' => 0,
 205         #         'CXGN::Page::Secretary' => 0,
 206         #         'CXGN::Page::Toolbar::SGN' => 0,
 207         #         'CXGN::Page::UserPrefs' => 0,
 208         #         'CXGN::Page::Widgets' => 0,
 209         #         'CXGN::People' => 0,
 210         #         'CXGN::People::BACStatusLog' => 0,
 211         #         'CXGN::People::Forum' => 0,
 212         #         'CXGN::People::Login' => 0,
 213         #         'CXGN::People::PageComment' => 0,
 214         #         'CXGN::People::Person' => 0,
 215         #         'CXGN::People::UserMap' => 0,
 216         #         'CXGN::People::UserMapData' => 0,
 217         #         'CXGN::Phenome' => 0,
 218         #         'CXGN::Phenome::Allele' => 0,
 219         #         'CXGN::Phenome::AlleleSynonym' => 0,
 220         #         'CXGN::Phenome::DbxrefType' => 0,
 221         #         'CXGN::Phenome::GenericGenePage' => 0,
 222         #         'CXGN::Phenome::Individual' => 0,
 223         #         'CXGN::Phenome::Individual::IndividualDbxref' => 0,
 224         #         'CXGN::Phenome::Individual::IndividualDbxrefEvidence' => 0,
 225         #         'CXGN::Phenome::Locus' => 0,
 226         #         'CXGN::Phenome::Locus::LinkageGroup' => 0,
 227         #         'CXGN::Phenome::Locus::LocusDbxrefEvidence' => 0,
 228         #         'CXGN::Phenome::Locus::LocusPage' => 0,
 229         #         'CXGN::Phenome::Locus::LocusRanking' => 0,
 230         #         'CXGN::Phenome::LocusDbxref' => 0,
 231         #         'CXGN::Phenome::LocusGroup' => 0,
 232         #         'CXGN::Phenome::LocusgroupMember' => 0,
 233         #         'CXGN::Phenome::LocusSynonym' => 0,
 234         #         'CXGN::Phenome::Main' => 0,
 235         #         'CXGN::Phenome::Population' => 0,
 236         #         'CXGN::Phenome::PopulationDbxref' => 0,
 237         #         'CXGN::Phenotypes' => 0,
 238         #         'CXGN::Phylo::Alignment' => 0,
 239         #         'CXGN::Phylo::Alignment::Member' => 0,
 240         #         'CXGN::Phylo::File' => 0,
 241         #         'CXGN::Phylo::Parser' => 0,
 242         #         'CXGN::Phylo::Tree' => 0,
 243         #         'CXGN::Phylo::Tree_browser' => 0,
 244         #         'CXGN::Publication' => 0,
 245         #         'CXGN::Publish' => 0,
 246         #         'CXGN::Scrap' => 0,
 247         #         'CXGN::Scrap::AjaxPage' => 0,
 248         #         'CXGN::Search::CannedForms' => 0,
 249         #         'CXGN::Searches::Family' => 0,
 250         #         'CXGN::Searches::Images' => 0,
 251         #         'CXGN::Searches::Library' => 0,
 252         #         'CXGN::Searches::People' => 0,
 253         #         'CXGN::Secretary::Family' => 0,
 254         #         'CXGN::Secretary::Gene' => 0,
 255         #         'CXGN::Secretary::Query' => 0,
 256         #         'CXGN::Sunshine::Browser' => 0,
 257         #         'CXGN::Sunshine::Node' => 0,
 258         #         'CXGN::Tag' => 0,
 259         #         'CXGN::TomatoGenome::BACPublish' => 0,
 260         #         'CXGN::TomatoGenome::BACSubmission' => 0,
 261         #         'CXGN::Tools::Entrez' => 0,
 262         #         'CXGN::Tools::FeatureFetch' => 0,
 263         #         'CXGN::Tools::File' => 0,
 264         #         'CXGN::Tools::File::Text' => 0,
 265         #         'CXGN::Tools::Gene' => 0,
 266         #         'CXGN::Tools::Identifiers' => 0,
 267         #         'CXGN::Tools::List' => 0,
 268         #         'CXGN::Tools::Organism' => 0,
 269         #         'CXGN::Tools::Param' => 0,
 270         #         'CXGN::Tools::Pubmed' => 0,
 271         #         'CXGN::Tools::Run' => 0,
 272         #         'CXGN::Tools::Script' => 0,
 273         #         'CXGN::Tools::Text' => 0,
 274         #         'CXGN::Tools::WebImageCache' => 0,
 275         #         'CXGN::Transcript::CDS' => 0,
 276         #         'CXGN::Transcript::EST' => 0,
 277         #         'CXGN::Transcript::Library' => 0,
 278         #         'CXGN::Transcript::Unigene' => 0,
 279         #         'CXGN::Transcript::UnigeneBuild' => 0,
 280         #         'CXGN::Unigene::Search' => 0,
 281         #         'CXGN::Unigene::Tools' => 0,
 282         #         'CXGN::UserList::Hotlist' => 0,
 283         #         'CXGN::UserPrefs' => 0,
 284         #        'DBI' => 0,
 285         'DBIx::Class'             => 0,
 286         'DBIx::Connector'         => 0,
 287         'File::Flock'             => 0,
 288         'File::NFSLock'           => 0,
 289         'File::Temp'              => 0,
 290         'Number::Bytes::Human'    => '0.07',
 291         'GD'                      => 0,
 292         'GD::Graph::Map'          => 0,
 293         'GD::Graph::points'       => 0,
 294         'GD::Text'                => 0,
 295         'HTML::Entities'          => 0,
 296         'HTML::Mason'             => 0,
 297         'IO::String'              => 0,
 298         'Image::Size'             => 0,
 299         'JSAN::ServerSide'        => '==0.06',
 300         'JSON'                    => 0,
 301         'JSON::XS'                => '2.24',
 302         'JSON::Any'               => 0,
 303         'List::Util'              => 0,
 304         'LWP::UserAgent'          => 0,
 305         'Mail::Sendmail'          => 0,
 306         'Math::Round::Var'        => 0,
 307         'Memoize'                 => 0,
 308         'Module::Build'           => '0.36',
 309         'Module::Find'            => 0,
 310         'Module::Pluggable::Object' => 0,
 311         'Moose'                   => 0,
 312         'MooseX::Declare'         => 0,
 313         'MooseX::Method::Signatures' => '0.30',
 314         'MooseX::Types::Path::Class' => 0,
 315         'MooseX::Types::URI'      => 0,
 316         'MooseX::Singleton'       => 0,
 317         'Number::Format'          => 0,
 318         'namespace::autoclean'    => 0,
 319         'SOAP::Transport::HTTP'   => 0,
 320         'Statistics::Descriptive' => 0,
 321         'Storable'                => 0,
 322         'Test::More'              => 0,
 323         'Test::Class'             => 0,
 324         'Test::WWW::Mechanize'    => 0,
 325         'Text::ParseWords'        => 0,
 326         'Tie::Function'           => 0,
 327         'Tie::UrlEncoder'         => 0,
 328         'Time::HiRes'             => 0,
 329         'Try::Tiny'               => 0,
 330         'URI'                     => 0,
 331         'URI::Escape'             => 0,
 332         'URI::FromHash'           => 0,
 333         'XML::Generator'          => 0,
 334         'XML::Twig'               => 0,
 335         'YAML::Any'               => 0,
 336         'File::Slurp'             => 0,
 337         'Test::JSON'              => 0,
 338         'Test::WWW::Mechanize::Catalyst' => 0,
 339     },
 340 );
 341 $build->create_build_script;
 342