Index: head/biology/abyss/Makefile
===================================================================
--- head/biology/abyss/Makefile	(revision 522850)
+++ head/biology/abyss/Makefile	(revision 522851)
@@ -1,39 +1,36 @@
 # $FreeBSD$
 
 PORTNAME=	abyss
-DISTVERSION=	2.1.5
-PORTREVISION=	6
+DISTVERSION=	2.2.3
 CATEGORIES=	biology
-MASTER_SITES=	http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/
 
-PATCH_SITES=	https://github.com/bcgsc/${PORTNAME}/commit/
-PATCHFILES=	25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch:-p1
-
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Assembly By Short Sequences: parallel, paired-end sequence assembler
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \
 		ghc:lang/ghc \
 		pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer
 LIB_DEPENDS=	libffi.so:devel/libffi \
 		libgmp.so:math/gmp \
 		libomp.so:devel/openmp
 RUN_DEPENDS=	bash:shells/bash \
 		gmake:devel/gmake
 
-USES=		compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
-SHEBANG_FILES=	bin/${PORTNAME}-*
+USES=		autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
+SHEBANG_FILES=	bin/${PORTNAME}-* DataBase/abyss-db-txt
 SHEBANG_LANG=	make
 make_OLD_CMD=	/usr/bin/make
 make_CMD=	${PREFIX}/bin/gmake
+USE_GITHUB=	yes
+GH_ACCOUNT=	bcgsc
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs
 
 OPTIONS_DEFINE=	DOCS
 
 PORTDOCS=	*
 
 .include <bsd.port.mk>
Index: head/biology/abyss/distinfo
===================================================================
--- head/biology/abyss/distinfo	(revision 522850)
+++ head/biology/abyss/distinfo	(revision 522851)
@@ -1,5 +1,3 @@
-TIMESTAMP = 1561103807
-SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757
-SIZE (abyss-2.1.5.tar.gz) = 1201318
-SHA256 (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 93ad66c42610c4fba8cfbe256a2ab689bf4a76974c3b97a9e1094863614ad934
-SIZE (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 1701
+TIMESTAMP = 1578886491
+SHA256 (bcgsc-abyss-2.2.3_GH0.tar.gz) = c7b93290b2ccffcf2f3ca42262621c636108f6dbc21f5684ebeeb4f682200675
+SIZE (bcgsc-abyss-2.2.3_GH0.tar.gz) = 1203318
Index: head/biology/abyss/pkg-plist
===================================================================
--- head/biology/abyss/pkg-plist	(revision 522850)
+++ head/biology/abyss/pkg-plist	(revision 522851)
@@ -1,60 +1,59 @@
 bin/ABYSS
 bin/ABYSS-P
 bin/AdjList
 bin/Consensus
 bin/DAssembler
 bin/DistanceEst
 bin/DistanceEst-ssq
 bin/KAligner
 bin/MergeContigs
 bin/MergePaths
 bin/Overlap
 bin/ParseAligns
 bin/PathConsensus
 bin/PathOverlap
 bin/PopBubbles
 bin/SimpleGraph
 bin/abyss-align
 bin/abyss-bloom
 bin/abyss-bloom-dbg
 bin/abyss-bloom-dist.mk
 bin/abyss-bowtie
 bin/abyss-bowtie2
 bin/abyss-bwa
 bin/abyss-bwamem
 bin/abyss-bwasw
 bin/abyss-db-csv
 bin/abyss-db-txt
 bin/abyss-dida
 bin/abyss-fac
 bin/abyss-fatoagp
 bin/abyss-filtergraph
 bin/abyss-fixmate
 bin/abyss-fixmate-ssq
 bin/abyss-gapfill
 bin/abyss-gc
 bin/abyss-index
 bin/abyss-junction
 bin/abyss-kaligner
 bin/abyss-layout
 bin/abyss-longseqdist
 bin/abyss-map
 bin/abyss-map-ssq
 bin/abyss-mergepairs
 bin/abyss-overlap
 bin/abyss-paired-dbg
 bin/abyss-pe
 bin/abyss-samtoafg
-bin/abyss-samtobreak
 bin/abyss-scaffold
 bin/abyss-sealer
 bin/abyss-stack-size
 bin/abyss-tabtomd
 bin/abyss-todot
 bin/abyss-tofastq
 bin/konnector
 bin/logcounter
 man/man1/ABYSS.1.gz
 man/man1/abyss-pe.1.gz
 man/man1/abyss-sealer.1.gz
 man/man1/abyss-tofastq.1.gz