https://github.com/genome/genome
Tip revision: 3fb56c777d039bdf4a7348262837db2d7436b467 authored by Dave Larson on 08 May 2013, 21:52:04 UTC
If we subtract one from the VCF coord then we need to add it back when
If we subtract one from the VCF coord then we need to add it back when
Tip revision: 3fb56c7
Build.PL
#!/usr/bin/env genome-perl
# Use local perl, not some perl on an application server!
use Config;
use Module::Build;
BEGIN {
unshift @INC, "$ENV{PWD}/blib/lib";
}
my $class = Module::Build->subclass (
class => 'Pod::Builder',
code => <<'EOS',
sub ACTION_clean {
# FIXME: is this safe?
use File::Path qw/rmtree/;
rmtree "./_build";
rmtree "./blib";
rmtree "./gmt-bindoc";
rmtree "./genome-bindoc";
unlink "./Build";
unlink "./MYMETA.yml";
}
sub ACTION_ur_docs {
use File::Copy qw/copy/;
$ENV{ANSI_COLORS_DISABLED} = 1;
eval {
local @INC = @INC;
unshift @INC, 'blib/lib';
die $@ if $@;
eval "use Genome::Search";
die $@ if $@;
foreach my $exec ('genome','gmt') {
UR::Namespace::Command::Update::Pod->execute(
class_name => 'Genome::Search',
executable_name => $exec,
targets => ['Genome::Search'],
output_path => 'cmd-bindoc'
);
}
};
die "failed to extract pod: $!: $@" if ($@);
}
sub ACTION_docs {
my $self = shift;
$self->depends_on('code');
#$self->depends_on('ur_docs');
$self->depends_on('manpages', 'html');
}
sub man1page_name {
my ($self, $file) = @_;
$file =~ s/.pod$//;
return $self->SUPER::man1page_name($file);
}
EOS
);
my $build = $class->new(
module_name => 'Genome::Search',
dist_version => 0.06,
license => 'lgpl',
requires => {
'perl' => 'v5.8.7',
'UR' => '0.29',
'Carp' => '',
'File::Basename' => '',
'File::Temp' => '',
'File::Find' => '',
'IO::File' => '',
'IO::String' => '',
'IO::Socket' => '',
'Sys::Hostname' => '',
'Plack' => '',
'Cache::Memcached' => '',
'AnyEvent' => '',
'Net::Server' => '',
'Starman' => '',
'Path::Class' => '',
'XML::LibXML' => '',
'XML::LibXSLT' => '',
'XML::Simple' => '',
},
cpan_client => 'cpanm',
etc_files => {
'etc/solr/solr-tomcat.xml' => 'solr/solr-tomcat.xml',
'etc/solr/tomcat.policy' => 'solr/tomcat.policy',
'etc/solr/web.xml' => 'solr/web.xml',
'etc/solr/conf/admin-extra.html' => 'solr/conf/admin-extra.html',
'etc/solr/conf/elevate.xml' => 'solr/conf/elevate.xml',
'etc/solr/conf/mapping-ISOLatin1Accent.txt' => 'solr/conf/mapping-ISOLatin1Accent.txt',
'etc/solr/conf/protwords.txt' => 'solr/conf/protwords.txt',
'etc/solr/conf/schema.xml' => 'solr/conf/schema.xml',
'etc/solr/conf/scripts.conf' => 'solr/conf/scripts.conf',
'etc/solr/conf/solrconfig.xml' => 'solr/conf/solrconfig.xml',
'etc/solr/conf/spellings.txt' => 'solr/conf/spellings.txt',
'etc/solr/conf/stopwords.txt' => 'solr/conf/stopwords.txt',
'etc/solr/conf/synonyms.txt' => 'solr/conf/synonyms.txt',
'etc/solr/conf/xslt/luke.xsl' => 'solr/conf/xslt/luke.xsl',
'etc/genome_solr.xml' => 'tomcat/genome_solr.xml',
'etc/genome' => 'apache/genome',
'etc/init/genome-task-runner.conf' => 'init/genome-task-runner.conf',
'etc/init/genome-search-index-queue.conf' => 'init/genome-search-index-queue.conf',
'etc/cron.daily/genome-task-cleanup.sh' => 'cron.daily/genome-task-cleanup.sh',
},
install_path => {
'solr' => '/var/cache/genome/solr/',
'apache' => '/etc/apache2/sites-available/',
'tomcat' => '/etc/tomcat6/Catalina/localhost/',
'init' => '/etc/init',
'cron.daily' => '/etc/cron.daily',
},
);
$build->add_build_element('psql');
$build->add_build_element('etc');
$build->add_build_element('solr');
$build->add_build_element('tomcat');
$build->add_build_element('apache');
$build->add_build_element('psgi');
$build->add_build_element('css');
$build->add_build_element('txt');
$build->add_build_element('png');
$build->add_build_element('html');
$build->add_build_element('jpg');
$build->add_build_element('gif');
$build->add_build_element('js');
$build->add_build_element('as');
$build->add_build_element('swf');
$build->add_build_element('sql');
$build->add_build_element('php');
$build->add_build_element('xsl');
$build->add_build_element('xml');
$build->add_build_element('conf');
$build->add_build_element('sh');
$build->create_build_script;