# $Id: Makefile.PL 1896 2011-06-06 14:49:23Z erick.antezana $
use 5.006;
use ExtUtils::MakeMaker;
# See lib/ExtUtils/MakeMaker.pm for details of how to influence
# the contents of the Makefile that is written.

$p = 'Date::Manip';
if (!eval "require $p") {
    print <<MSG;

   Date::Manip is missing. This module is required in order to perform 
   dates checking while parsing OBO-formatted files (e.g. 'creation_date' tag).
   However, this module is not fully required for using ONTO-PERL. If you 
   do not intend to parse OBO-formatted files, then you may continue, and 
   install Date::Manip in the future.

MSG
      
}

$p = 'SWISS::Entry';
if (!eval "require $p") {
    print <<MSG;

   SWISS::Entry is missing. This module is only required in order to
   perform parsing operations with UniProt files. However, this 
   module is not required for using ONTO-PERL. If you do not intend 
   to use UniProt files, then you may continue, and install 
   SWISS::Entry in the future.

MSG
      
}

$p = 'XML::Parser';
if (!eval "require $p") {
    print <<MSG;

   XML::Parser is missing. This module is only required in order to
   perform parsing operations with XML files (obo2owl). However, this 
   module is not fully required for using ONTO-PERL. If you do not intend 
   to convert your files to OWL, then you may continue, and install 
   XML::Parser in the future.

MSG
      
}

$p = 'XML::XPath';
if (!eval "require $p") {
    print <<MSG;

   XML::XPath is missing. This module is only required in order to
   perform parsing operations with IntAct-XML files. However, this 
   module is not required for using ONTO-PERL. If you do not intend 
   to use IntAct XML files, then you may continue, and install 
   XML::XPath in the future.

MSG
      
}

my @license = $ExtUtils::MakeMaker::VERSION > 6.30
? qw(LICENSE perl)
: ();


WriteMakefile(
	NAME              => 'ONTO-PERL',
	DISTNAME          => 'ONTO-PERL',
	ABSTRACT          => 'PERL modules for manipulating OBO-formatted ontologies, such as the Gene Ontology (GO)',
	VERSION_FROM      => 'lib/OBO/Core/Ontology.pm',
	@license,
	PREREQ_PM         => {
						'Date::Manip'   => 6.24,
						#'SWISS::Entry' => 1.67, # optional
						#'XML::Parser'  => 2.41, # optional
						#'XML::XPath'   => 1.13  # optional
						},
	EXE_FILES         => [
							qw(
								scripts/get_ancestor_terms.pl
								scripts/get_child_terms.pl
								scripts/get_descendent_terms.pl
								scripts/get_lowest_common_ancestor.pl
								scripts/get_obsolete_term_id_vs_def_in_go.pl
								scripts/get_obsolete_term_id_vs_name_in_go.pl
								scripts/get_obsolete_terms.pl
								scripts/get_parent_terms.pl
								scripts/get_relationship_id_vs_relationship_def.pl
								scripts/get_relationship_id_vs_relationship_name.pl
								scripts/get_relationship_id_vs_relationship_namespace.pl
								scripts/get_relationship_types.pl
								scripts/get_root_terms.pl
								scripts/get_subontology_from.pl
								scripts/get_term_id_vs_term_def.pl
								scripts/get_term_id_vs_term_name.pl
								scripts/get_term_id_vs_term_namespace.pl
								scripts/get_term_local_neighbourhood.pl
								scripts/get_term_synonyms.pl
								scripts/get_terms.pl
								scripts/get_terms_and_synonyms.pl
								scripts/get_terms_by_name.pl
								scripts/go2owl.pl
								scripts/goa2rdf.pl
								scripts/obo2apo.pl
								scripts/obo2owl.pl
								scripts/obo2rdf.pl
								scripts/obo2tran.pl	
								scripts/obo2xml.pl
								scripts/obo_intersection.pl
								scripts/obo_transitive_reduction.pl
								scripts/obo_trimming.pl
								scripts/obo_union.pl
								scripts/owl2obo.pl
							)
						],
			
	($] >= 5.005 ?     ## Add these new keywords supported since 5.005
	(AUTHOR   => 'Erick Antezana <erick.antezana -@- gmail.com>') : ()),
	dist      => { 
					'SUFFIX'       => '.gz',
					'DIST_DEFAULT' => 'all tardist',
					'COMPRESS'     => 'gzip -9f' 
				},
	clean      => {FILES => "t/data/human.2.map
							t/data/add_goa_assocs.out
							t/data/goa.rdf
							t/data/goa_parser_test_out.obo
							t/data/go.obo
							t/data/go_transitive_closure.obo
							t/data/go_transitive_reduction.obo
							t/data/intact_parser_test_out.obo
							t/data/ncbi.rdf
							t/data/ncbi_parser_test_out.obo
							t/data/pre_apo_taxa.obo
							t/data/test0.obo
							t/data/test1.obo
							t/data/test1.rdf
							t/data/test1.xml
							t/data/test2.dot
							t/data/test2.obo
							t/data/test2.owl
							t/data/test2.rdf
							t/data/test2.xml
							t/data/test_ulo_apo2.obo
							t/data/test_ulo_apo.dot
							t/data/test_ulo_apo.owl
							t/data/uniprot_parser_test_out.obo"},
);