Update biology/bioperl to 1.6.923.

Way too many changes (0.7.0 was released in 2001!).

See changelog at:

https://github.com/bioperl/bioperl-live/blob/master/Changes

6 files changed, 153 insertions, 133 deletions

diff --git a/biology/bioperl/DESCR b/biology/bioperl/DESCR
index 213f3419102..3bd07299f7f 100644
--- a/biology/bioperl/DESCR
+++ b/biology/bioperl/DESCR
@@ -1,11 +1,6 @@
-  The Bioperl project is a coordinated effort to collect computational
-methods routinely used in bioinformatics into a set of standard
-CPAN-style, well-documented, and freely available Perl modules.  Perl
-provides unparalleled support for many tasks common in bioinformatics
-yet there are no standard Perl modules for biology.  Bioperl hopes to
-help fill this void.
+The Bioperl Project is an international association of developers of open
+source Perl tools for bioinformatics, genomics and life science research.
 
-  Bioperl modules and source code will always be freely available
-under the same terms as Perl itself.  The Bioperl project is open to
-all and we invite suggestions and participation from the larger
-bioinformatics community.
+Bioperl is a collection of object-oriented Perl modules created by the
+Bioperl Project.  It forms the basis of a large number of bioinformatics
+and genomics applications.
diff --git a/biology/bioperl/Makefile b/biology/bioperl/Makefile
index 04ea1a136aa..882e27bf254 100644
--- a/biology/bioperl/Makefile
+++ b/biology/bioperl/Makefile
@@ -1,33 +1,64 @@
-# $NetBSD: Makefile,v 1.24 2013/05/31 12:39:38 wiz Exp $
-#
-
-DISTNAME=		bioperl-0.7.0
-PKGREVISION=		7
-CATEGORIES=		biology
-MASTER_SITES=		http://bioperl.org/DIST/old_releases/
-
-MAINTAINER=		pkgsrc-users@NetBSD.org
-HOMEPAGE=		http://bioperl.org/
-COMMENT=		Perl tools for computational molecular biology
-
-USE_TOOLS+=	pax
-
-REPLACE_PERL+=		Bio/LiveSeq/Chain.pm
-REPLACE_PERL+=		Bio/SeqIO/game/featureHandler.pm
-REPLACE_PERL+=		Bio/Tools/Blast/Run/postclient.pl
-REPLACE_PERL+=		examples/gsequence
-REPLACE_PERL+=		examples/*.pl
-REPLACE_PERL+=		examples/blast/*.pl
-REPLACE_PERL+=		examples/root_object/*.pl
-REPLACE_PERL+=		examples/root_object/vector/vector.pl
-REPLACE_PERL+=		examples/seq/*.pl
+# $NetBSD: Makefile,v 1.25 2014/02/20 14:44:16 fhajny Exp $
 
+DISTNAME=	BioPerl-1.6.923
+PKGNAME=	${DISTNAME:tl}
+CATEGORIES=	biology perl5
+MASTER_SITES=	${MASTER_SITE_PERL_CPAN:=Bio/}
+
+MAINTAINER=	filip@joyent.com
+HOMEPAGE=	http://www.bioperl.org/
+COMMENT=	Perl tools for computational molecular biology
+LICENSE=	${PERL5_LICENSE}
+
+BUILD_DEPENDS+=	p5-Module-Build>0.42:../../devel/p5-Module-Build
+BUILD_DEPENDS+=	p5-Test-Most-[0-9]*:../../devel/p5-Test-Most
+
+DEPENDS+=	p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres
+DEPENDS+=	p5-Array-Compare-[0-9]*:../../devel/p5-Array-Compare
+DEPENDS+=	p5-Bio-ASN1-EntrezGene-[0-9]*:../../biology/p5-Bio-ASN1-EntrezGene
+DEPENDS+=	p5-Clone-[0-9]*:../../devel/p5-Clone
+DEPENDS+=	p5-Convert-Binary-C-[0-9]*:../../devel/p5-Convert-Binary-C
+DEPENDS+=	p5-DB_File-[0-9]*:../../databases/p5-DB_File
+DEPENDS+=	p5-Data-Stag>=0.11:../../devel/p5-Data-Stag
+DEPENDS+=	p5-Error-[0-9]*:../../devel/p5-Error
+DEPENDS+=	p5-ExtUtils-Manifest>=1.52:../../devel/p5-ExtUtils-Manifest
+DEPENDS+=	p5-GD-[0-9]*:../../graphics/p5-GD
+DEPENDS+=	p5-Graph>=0.50:../../devel/p5-Graph
+DEPENDS+=	p5-GraphViz-[0-9]*:../../graphics/p5-GraphViz
+DEPENDS+=	p5-HTML-Parser>=3:../../www/p5-HTML-Parser
+DEPENDS+=	p5-HTML-TableExtract-[0-9]*:../../www/p5-HTML-TableExtract
+DEPENDS+=	p5-IO-String-[0-9]*:../../devel/p5-IO-String
+DEPENDS+=	p5-List-MoreUtils-[0-9]*:../../devel/p5-List-MoreUtils
+DEPENDS+=	p5-PostScript-[0-9]*:../../print/p5-PostScript
+DEPENDS+=	p5-SOAP-Lite-[0-9]*:../../net/p5-SOAP-Lite
+DEPENDS+=	p5-SVG-Graph>=0.01:../../graphics/p5-SVG-Graph
+DEPENDS+=	p5-SVG>=2.26:../../graphics/p5-SVG
+DEPENDS+=	p5-Set-Scalar-[0-9]*:../../devel/p5-Set-Scalar
+DEPENDS+=	p5-Sort-Naturally-[0-9]*:../../devel/p5-Sort-Naturally
+DEPENDS+=	p5-Spreadsheet-ParseExcel-[0-9]*:../../math/p5-Spreadsheet-ParseExcel
+DEPENDS+=	p5-Storable>=2.05:../../devel/p5-Storable
+DEPENDS+=	p5-XML-Parser-[0-9]*:../../textproc/p5-XML-Parser
+DEPENDS+=	p5-XML-SAX-Writer-[0-9]*:../../textproc/p5-XML-SAX-Writer
+DEPENDS+=	p5-XML-SAX>=0.15:../../textproc/p5-XML-SAX
+DEPENDS+=	p5-XML-Simple-[0-9]*:../../textproc/p5-XML-Simple
+DEPENDS+=	p5-XML-Twig-[0-9]*:../../textproc/p5-XML-Twig
+DEPENDS+=	p5-XML-Writer>=0.4:../../textproc/p5-XML-Writer
+DEPENDS+=	p5-YAML-[0-9]*:../../textproc/p5-YAML
+DEPENDS+=	p5-libwww-[0-9]*:../../www/p5-libwww
+DEPENDS+=	p5-libxml-[0-9]*:../../textproc/p5-libxml
+
+USE_TOOLS+=		pax
+
+REPLACE_PERL+=		scripts/*/*.pl
+
+PERL5_MODULE_TYPE=	Module::Build
 PERL5_PACKLIST=		auto/Bio/.packlist
 
 INSTALLATION_DIRS=	share/examples/bioperl
 
 post-install:
-	cd ${WRKSRC}/examples && pax -rw . ${DESTDIR}${PREFIX}/share/examples/bioperl
+	cd ${WRKSRC}/examples && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/bioperl
 
+.include "options.mk"
 .include "../../lang/perl5/module.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/bioperl/PLIST b/biology/bioperl/PLIST
index 22976d99fe5..4e2abdf7029 100644
--- a/biology/bioperl/PLIST
+++ b/biology/bioperl/PLIST
@@ -1,74 +1,62 @@
-@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
-share/examples/bioperl/blast/out/blastn.2.gz
-share/examples/bioperl/blast/out/blastn.2.wu.gz
-share/examples/bioperl/blast/out/blastp.1.gcg.gz
-share/examples/bioperl/blast/out/blastp.1.gz
-share/examples/bioperl/blast/out/blastp.2.gz
-share/examples/bioperl/blast/out/blastp.2.nogap.gz
-share/examples/bioperl/blast/out/blastp.2.wu
-share/examples/bioperl/blast/out/blastp.205.gz
-share/examples/bioperl/blast/out/blastp.2a.gz
-share/examples/bioperl/blast/out/blastp.2b.gz
-share/examples/bioperl/blast/out/blastp.email.html.gz
-share/examples/bioperl/blast/out/blastx.2
-share/examples/bioperl/blast/out/blastx.2.email.gz
-share/examples/bioperl/blast/out/blastx.208.gz
-share/examples/bioperl/blast/out/tblastn.206.out.gz
-share/examples/bioperl/blast/seq/acc1.dna.fasta
-share/examples/bioperl/blast/seq/seqs.fasta
-share/examples/bioperl/blast/seq/yal011w.dna.fasta
-share/examples/bioperl/blast/seq/yel009c.fasta
-share/examples/bioperl/blast/seq/ymr284w.fasta
-share/examples/bioperl/blast/blast_config.pl
-share/examples/bioperl/blast/blast_seq.pl
-share/examples/bioperl/blast/example.table1
-share/examples/bioperl/blast/example.table2
-share/examples/bioperl/blast/html.pl
-share/examples/bioperl/blast/parse_blast.pl
-share/examples/bioperl/blast/parse_blast2.pl
-share/examples/bioperl/blast/parse_multi.pl
-share/examples/bioperl/blast/parse_positions.pl
-share/examples/bioperl/blast/print_blasts.pl
-share/examples/bioperl/blast/retrieve_blast.pl
-share/examples/bioperl/blast/run_blast_remote.pl
-share/examples/bioperl/blosum62.bla
-share/examples/bioperl/change_gene.pl
-share/examples/bioperl/clustalw.pl
-share/examples/bioperl/getGenBank.pl
-share/examples/bioperl/gon250.bla
-share/examples/bioperl/gsequence
-share/examples/bioperl/hitdisplay.pl
-share/examples/bioperl/psw.pl
-share/examples/bioperl/restriction.pl
+@comment $NetBSD: PLIST,v 1.3 2014/02/20 14:44:16 fhajny Exp $
+share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl
+share/examples/bioperl/align/FastAlign.pl
+share/examples/bioperl/align/align_on_codons.pl
+share/examples/bioperl/align/aligntutorial.pl
+share/examples/bioperl/align/clustalw.pl
+share/examples/bioperl/align/simplealign.pl
+share/examples/bioperl/bioperl.pl
+share/examples/bioperl/cluster/dbsnp.pl
+share/examples/bioperl/contributed/nmrpdb_parse.pl
+share/examples/bioperl/contributed/prosite2perl.pl
+share/examples/bioperl/contributed/rebase2list.pl
+share/examples/bioperl/db/dbfetch
+share/examples/bioperl/db/est_tissue_query.pl
+share/examples/bioperl/db/gb2features.pl
+share/examples/bioperl/db/getGenBank.pl
+share/examples/bioperl/db/get_seqs.pl
+share/examples/bioperl/db/rfetch.pl
+share/examples/bioperl/db/use_registry.pl
+share/examples/bioperl/generate_random_seq.pl
+share/examples/bioperl/liveseq/change_gene.pl
+share/examples/bioperl/longorf.pl
+share/examples/bioperl/make_primers.pl
+share/examples/bioperl/popgen/parse_calc_stats.pl
+share/examples/bioperl/quality/svgtrace.pl
 share/examples/bioperl/rev_and_trans.pl
-share/examples/bioperl/seq_pattern.pl
-share/examples/bioperl/simplealign.pl
-share/examples/bioperl/standaloneblast.pl
-share/examples/bioperl/test-genscan.pl
-share/examples/bioperl/root_object/Outer.pm
-share/examples/bioperl/root_object/Bar.pm
-share/examples/bioperl/root_object/Foo.pm
-share/examples/bioperl/root_object/vector/Person.pm
-share/examples/bioperl/root_object/vector/PersonManager.pm
-share/examples/bioperl/root_object/vector/vector.out
-share/examples/bioperl/root_object/vector/vector.pl
-share/examples/bioperl/root_object/destroy.pl
-share/examples/bioperl/root_object/error.out
-share/examples/bioperl/root_object/error.pl
-share/examples/bioperl/root_object/filehandle.out
-share/examples/bioperl/root_object/filehandle.pl
-share/examples/bioperl/root_object/io.out
-share/examples/bioperl/root_object/io.pl
-share/examples/bioperl/root_object/read.pl
-share/examples/bioperl/root_object/read.test
-share/examples/bioperl/root_object/read.test2
-share/examples/bioperl/root_object/read.test3
-share/examples/bioperl/root_object/utilities.pl
-share/examples/bioperl/seq/seq.fasta.gz
-share/examples/bioperl/seq/id.list
-share/examples/bioperl/seq/seq1.fasta
-share/examples/bioperl/seq/seq2.fasta
-share/examples/bioperl/seq/seqs1.pl
-share/examples/bioperl/seq/seqs2.pl
-share/examples/bioperl/seq/seqs3.pl
-share/examples/bioperl/seq/seqtools.pl
+share/examples/bioperl/revcom_dir.pl
+share/examples/bioperl/root/README
+share/examples/bioperl/root/exceptions1.pl
+share/examples/bioperl/root/exceptions2.pl
+share/examples/bioperl/root/exceptions3.pl
+share/examples/bioperl/root/exceptions4.pl
+share/examples/bioperl/root/lib/TestInterface.pm
+share/examples/bioperl/root/lib/TestObject.pm
+share/examples/bioperl/searchio/blast_example.pl
+share/examples/bioperl/searchio/custom_writer.pl
+share/examples/bioperl/searchio/hitwriter.pl
+share/examples/bioperl/searchio/hspwriter.pl
+share/examples/bioperl/searchio/htmlwriter.pl
+share/examples/bioperl/searchio/psiblast_features.pl
+share/examples/bioperl/searchio/psiblast_iterations.pl
+share/examples/bioperl/searchio/rawwriter.pl
+share/examples/bioperl/searchio/resultwriter.pl
+share/examples/bioperl/searchio/waba2gff.pl
+share/examples/bioperl/searchio/waba2gff3.pl
+share/examples/bioperl/sirna/TAG
+share/examples/bioperl/sirna/rnai_finder.cgi
+share/examples/bioperl/structure/structure-io.pl
+share/examples/bioperl/subsequence.cgi
+share/examples/bioperl/tk/gsequence.pl
+share/examples/bioperl/tk/hitdisplay.pl
+share/examples/bioperl/tools/extract_genes.pl
+share/examples/bioperl/tools/gb_to_gff.pl
+share/examples/bioperl/tools/gff2ps.pl
+share/examples/bioperl/tools/parse_codeml.pl
+share/examples/bioperl/tools/psw.pl
+share/examples/bioperl/tools/reverse-translate.pl
+share/examples/bioperl/tools/run_genscan.pl
+share/examples/bioperl/tools/run_primer3.pl
+share/examples/bioperl/tools/seq_pattern.pl
+share/examples/bioperl/tools/standaloneblast.pl
+share/examples/bioperl/tree/paup2phylip.pl
diff --git a/biology/bioperl/distinfo b/biology/bioperl/distinfo
index bfc2f7d9e35..d23a048951e 100644
--- a/biology/bioperl/distinfo
+++ b/biology/bioperl/distinfo
@@ -1,6 +1,5 @@
-$NetBSD: distinfo,v 1.4 2006/10/02 21:34:28 rillig Exp $
+$NetBSD: distinfo,v 1.5 2014/02/20 14:44:16 fhajny Exp $
 
-SHA1 (bioperl-0.7.0.tar.gz) = c86abeeb5f2e2b98d1577d9cefd51ce15bbcb6b6
-RMD160 (bioperl-0.7.0.tar.gz) = 41c4162d8d8ec5b406ba34d0d48702700d62108d
-Size (bioperl-0.7.0.tar.gz) = 1329985 bytes
-SHA1 (patch-aa) = 2e1064f4d7c343cf62f53f2a179a3a1841220dc7
+SHA1 (BioPerl-1.6.923.tar.gz) = eacdb736820efad9205a9ed2150190d7ee89a5ed
+RMD160 (BioPerl-1.6.923.tar.gz) = d111ceb0dd60ccef1473e378f4ed8d67dad6013e
+Size (BioPerl-1.6.923.tar.gz) = 12562520 bytes
diff --git a/biology/bioperl/options.mk b/biology/bioperl/options.mk
new file mode 100644
index 00000000000..b4544c146ca
--- /dev/null
+++ b/biology/bioperl/options.mk
@@ -0,0 +1,28 @@
+# $NetBSD: options.mk,v 1.1 2014/02/20 14:44:16 fhajny Exp $
+
+PKG_OPTIONS_VAR=	PKG_OPTIONS.bioperl
+PKG_SUPPORTED_OPTIONS+=	mysql pgsql sqlite
+
+.include "../../mk/bsd.options.mk"
+
+###
+### MySQL support
+###
+.if !empty(PKG_OPTIONS:Mmysql)
+.include "../../mk/mysql.buildlink3.mk"
+DEPENDS+=		p5-DBD-${MYSQL_PKG_PREFIX}-[0-9]*:../../databases/p5-DBD-mysql
+.endif
+
+###
+### PostgreSQL support
+###
+.if !empty(PKG_OPTIONS:Mpgsql)
+DEPENDS+=		p5-DBD-postgresql-[0-9]*:../../databases/p5-DBD-postgresql
+.endif
+
+###
+### SQLite support
+###
+.if !empty(PKG_OPTIONS:Msqlite)
+DEPENDS+=		p5-DBD-SQLite-[0-9]*:../../databases/p5-DBD-SQLite
+.endif
diff --git a/biology/bioperl/patches/patch-aa b/biology/bioperl/patches/patch-aa
deleted file mode 100644
index caf202de248..00000000000
--- a/biology/bioperl/patches/patch-aa
+++ /dev/null
@@ -1,21 +0,0 @@
-$NetBSD: patch-aa,v 1.3 2006/10/02 21:34:28 rillig Exp $
-
-If LWP::UserAgent is not available, exit before the module is required
-implicitly by Bio::DB::GDB.
-
---- t/GDB.t.orig	2001-03-01 10:11:15.000000000 +0100
-+++ t/GDB.t	2006-10-02 23:30:15.000000000 +0200
-@@ -33,10 +33,9 @@ BEGIN {
- 	foreach ( 1..$NUMTESTS) { skip(1,1); }
- 	$error = 1;
-     }
--}
--
--if( $error == 1 ) {
--    exit(0);
-+    if( $error == 1 ) {
-+	exit(0);
-+    }
- }
- 
- use Bio::DB::GDB;