--- seqan-apps/distinfo	2016-09-14 21:38:58.000000000 +0200
+++ seqan-apps/distinfo	2018-02-14 17:54:28.261623000 +0100
@@ -1,3 +1,3 @@ 
-TIMESTAMP = 1473848209
-SHA256 (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8
-SIZE (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 110936119
+TIMESTAMP = 1517833288
+SHA256 (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7
+SIZE (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = 109626901
--- seqan-apps/Makefile	2018-01-18 05:11:02.000000000 +0100
+++ seqan-apps/Makefile	2018-02-14 18:06:39.749270000 +0100
@@ -2,34 +2,34 @@ 
 # $FreeBSD: head/biology/seqan-apps/Makefile 459315 2018-01-18 04:11:02Z jbeich $
 
 PORTNAME=	seqan-apps
-PORTVERSION=	2.2.0
 DISTVERSIONPREFIX=	seqan-v
-PORTREVISION=	9
+DISTVERSION=	2.4.0
 CATEGORIES=	biology
 
 MAINTAINER=	h2+fbsdports@fsfe.org
-COMMENT=	Official Bioinformatic applications based on the SeqAn library
+COMMENT=	Official bioinformatic applications based on the SeqAn library
 
 LICENSE=	BSD3CLAUSE LGPL3 GPLv3
 LICENSE_COMB=	multi
 
 BUILD_DEPENDS=	boost-libs>0:devel/boost-libs
 
-BROKEN_aarch64=		fails to compile: Error: unknown mnemonic rep -- rep
-BROKEN_armv6=		fails to compile: Error: bad instruction rep
-BROKEN_armv7=		fails to compile: Error: bad instruction rep
-BROKEN_powerpc64=	fails to compile: Error: unrecognized opcode: rep
-
+# once #199603 is resolved, add c++14-lang:
+# USES=		cmake:outsource compiler:openmp,c++14-lang
+USES=		cmake:outsource compiler:openmp
 USE_GITHUB=	yes
 GH_ACCOUNT=	seqan
 GH_PROJECT=	seqan
-
-# once #199603 is resolved, do the following instead of USE_GCC
-# USES=		cmake:outsource compiler:openmp,c++14-lang
-USES=		cmake:outsource
 CMAKE_ARGS=	-DSEQAN_BUILD_SYSTEM="SEQAN_RELEASE_APPS"
 
-USE_GCC=	yes
+OPTIONS_RADIO=		ARCH
+OPTIONS_RADIO_ARCH=	SSE4 AVX2 NATIVE
+SSE4_DESC= 		Use SSE4 and POPCNT instructions
+SSE4_CMAKE_ON=		-DSEQAN_ARCH_SSE4:BOOL=TRUE
+AVX2_DESC= 		Use SSE4, AVX2 and POPCNT instructions
+AVX2_CMAKE_ON=		-DSEQAN_ARCH_AVX2:BOOL=TRUE
+NATIVE_DESC=		Use all available instruction sets (-march=native)
+NATIVE_CMAKE_ON=	-DSEQAN_ARCH_NATIVE:BOOL=TRUE
 
 .include <bsd.port.pre.mk>
 
--- seqan-apps/pkg-plist	2016-05-10 02:52:04.000000000 +0200
+++ seqan-apps/pkg-plist	2018-02-14 17:54:28.262215000 +0100
@@ -48,6 +48,7 @@ 
 bin/tree_recon
 bin/yara_indexer
 bin/yara_mapper
+man/man1/sak.1.gz
 share/doc/alf/LICENSE
 share/doc/alf/README
 share/doc/alf/example/small.fasta
@@ -117,7 +118,6 @@ 
 share/doc/sak/LICENSE
 share/doc/sak/README
 share/doc/sak/README.sak.txt
-share/doc/sak/man/sak.1
 share/doc/sam2matrix/LICENSE
 share/doc/sam2matrix/README
 share/doc/samcat/LICENSE