Index: head/biology/abyss/Makefile
===================================================================
--- head/biology/abyss/Makefile
+++ head/biology/abyss/Makefile
@@ -6,6 +6,9 @@
 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
 
@@ -21,7 +24,7 @@
 RUN_DEPENDS=	bash:shells/bash \
 		gmake:devel/gmake
 
-USES=		gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
+USES=		compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
 SHEBANG_FILES=	bin/${PORTNAME}-*
 SHEBANG_LANG=	make
 make_OLD_CMD=	/usr/bin/make
Index: head/biology/abyss/distinfo
===================================================================
--- head/biology/abyss/distinfo
+++ head/biology/abyss/distinfo
@@ -1,3 +1,5 @@
-TIMESTAMP = 1551061546
+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
Index: head/biology/abyss/files/patch-Common_city.cc
===================================================================
--- head/biology/abyss/files/patch-Common_city.cc
+++ head/biology/abyss/files/patch-Common_city.cc
@@ -0,0 +1,13 @@
+--- Common/city.cc.orig	2018-09-21 23:44:14 UTC
++++ Common/city.cc
+@@ -65,6 +65,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) {
+ #define bswap_32(x) OSSwapInt32(x)
+ #define bswap_64(x) OSSwapInt64(x)
+ 
++#elif defined(__FreeBSD__)
++#include <sys/endian.h>
++#define bswap_32(x) bswap32(x)
++#define bswap_64(x) bswap64(x)
+ #else
+ #include <byteswap.h>
+ #endif