biology/mummer: Update 3.23 -> 4.0.0beta2-2

Port changes:
* Moved to github
* It now installs itself
* It uses yaggo during build

3 files changed, 61 insertions, 47 deletions

diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index fb1fc39533e5..bec600c91b36 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -2,46 +2,28 @@
 # $FreeBSD$
 
 PORTNAME=	mummer
-PORTVERSION=	3.23
-PORTREVISION=	2
+DISTVERSIONPREFIX=	v
+DISTVERSION=	4.0.0beta2-2
+DISTVERSIONSUFFIX=	-g277dac5
 CATEGORIES=	biology
-MASTER_SITES=	SF
-DISTNAME=	MUMmer${PORTVERSION}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Modular system for rapid whole genome alignment
 
 LICENSE=	ART10
-LICENSE_FILE=	${WRKSRC}/LICENSE
+LICENSE_FILE=	${WRKSRC}/LICENSE.md
 
-USES=		gmake perl5 shebangfix
+BUILD_DEPENDS=	yaggo:devel/yaggo
 
-SHEBANG_FILES=	scripts/*.csh scripts/*.pl
-SHEBANG_LANG=	csh
+USES=		autoreconf gmake libtool perl5 shebangfix
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--disable-static
+USE_GITHUB=	yes
+GH_ACCOUNT=	${PORTNAME}4
+USE_LDCONFIG=	yes
+
+SHEBANG_FILES=	scripts/*.pl
 perl_OLD_CMD=	__PERL_PATH
-csh_OLD_CMD=	__CSH_PATH
-csh_CMD=	/bin/csh
 _SHEBANG_REINPLACE_ARGS+=	-e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g"
 
-PROGRAMS=	annotate combineMUMs delta-filter gaps \
-		mgaps mummer repeat-match show-aligns \
-		show-coords show-diff show-snps show-tiling
-SCRIPTS=	dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \
-		nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh
-LIBEXEC=	Foundation.pm tandem-repeat.awk
-DOCUMENTS=	COPYRIGHT INSTALL LICENSE README
-
-OPTIONS_DEFINE=	DOCS
-
-do-install:
-	${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin
-.for file in ${SCRIPTS}
-	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R}
-.endfor
-	@${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
-	${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
-	${INSTALL_DATA} ${LIBEXEC:S|^|${WRKSRC}/scripts/|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME}
-	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR}
-
 .include <bsd.port.mk>
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
index f291784990f0..fbf62e1b29dd 100644
--- a/biology/mummer/distinfo
+++ b/biology/mummer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1509357521
-SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f
-SIZE (MUMmer3.23.tar.gz) = 3160143
+TIMESTAMP = 1544513160
+SHA256 (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 4b77fb57f0e7994ed0cb9886de23ce620b89cb16734df82ba492dbc750e387f1
+SIZE (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 18369428
diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist
index 53b5159185a0..8e4946d83c05 100644
--- a/biology/mummer/pkg-plist
+++ b/biology/mummer/pkg-plist
@@ -3,29 +3,61 @@ bin/combineMUMs
 bin/delta-filter
 bin/dnadiff
 bin/exact-tandems
-bin/gaps
-bin/mapview
-bin/mgaps
 bin/mummer
 bin/mummerplot
 bin/nucmer
-bin/nucmer2xfig
 bin/promer
 bin/repeat-match
-bin/run-mummer1
-bin/run-mummer3
 bin/show-aligns
 bin/show-coords
 bin/show-diff
 bin/show-snps
 bin/show-tiling
-libexec/mummer/Foundation.pm
+include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort.hpp
+include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort_imp.hpp
+include/mummer-4.0.0beta2/include/compactsufsort/const_iterator_traits.hpp
+include/mummer-4.0.0beta2/include/compactsufsort/divsufsort_private.h
+include/mummer-4.0.0beta2/include/compactsufsort/said_traits.hpp
+include/mummer-4.0.0beta2/include/compactsufsort/sssort_imp.hpp
+include/mummer-4.0.0beta2/include/compactsufsort/trsort_imp.hpp
+include/mummer-4.0.0beta2/include/jellyfish/circular_buffer.hpp
+include/mummer-4.0.0beta2/include/jellyfish/cooperative_pool2.hpp
+include/mummer-4.0.0beta2/include/jellyfish/cpp_array.hpp
+include/mummer-4.0.0beta2/include/jellyfish/divisor.hpp
+include/mummer-4.0.0beta2/include/jellyfish/stream_manager.hpp
+include/mummer-4.0.0beta2/include/jellyfish/whole_sequence_parser.hpp
+include/mummer-4.0.0beta2/include/mt_skip_list/common.hpp
+include/mummer-4.0.0beta2/include/mt_skip_list/set.hpp
+include/mummer-4.0.0beta2/include/mummer/48bit_index.hpp
+include/mummer-4.0.0beta2/include/mummer/48bit_iterator.hpp
+include/mummer-4.0.0beta2/include/mummer/const_iterator_traits.hpp
+include/mummer-4.0.0beta2/include/mummer/delta.hh
+include/mummer-4.0.0beta2/include/mummer/dset.hpp
+include/mummer-4.0.0beta2/include/mummer/fasta.hpp
+include/mummer-4.0.0beta2/include/mummer/mgaps.hh
+include/mummer-4.0.0beta2/include/mummer/nucmer.hpp
+include/mummer-4.0.0beta2/include/mummer/openmp_qsort.hpp
+include/mummer-4.0.0beta2/include/mummer/postnuc.hh
+include/mummer-4.0.0beta2/include/mummer/redirect_to_pager.hpp
+include/mummer-4.0.0beta2/include/mummer/sparseSA.hpp
+include/mummer-4.0.0beta2/include/mummer/sparseSA_imp.hpp
+include/mummer-4.0.0beta2/include/mummer/sw_align.hh
+include/mummer-4.0.0beta2/include/mummer/sw_alignscore.hh
+include/mummer-4.0.0beta2/include/mummer/tigrinc.hh
+include/mummer-4.0.0beta2/include/mummer/timer.hpp
+include/mummer-4.0.0beta2/include/mummer/translate.hh
+include/mummer-4.0.0beta2/include/thread_pipe.hpp
+include/mummer-4.0.0beta2/include/thread_pipe/circular_buffer.hpp
+include/mummer-4.0.0beta2/include/thread_pipe/cooperative_pool2.hpp
+include/mummer-4.0.0beta2/include/thread_pipe/divisor.hpp
+include/mummer-4.0.0beta2/include/thread_pipe/traits.hpp
+lib/libumdmummer.so
+lib/libumdmummer.so.0
+lib/libumdmummer.so.0.0.0
+lib/mummer/Foundation.pm
+lib/mummer/tandem-repeat.awk
+libdata/pkgconfig/mummer.pc
+libexec/mummer/mgaps
 libexec/mummer/postnuc
 libexec/mummer/postpro
-libexec/mummer/prenuc
 libexec/mummer/prepro
-libexec/mummer/tandem-repeat.awk
-%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL
-%%PORTDOCS%%%%DOCSDIR%%/LICENSE
-%%PORTDOCS%%%%DOCSDIR%%/README