6 files changed, 116 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index f680a6304fc1..1200763e5abf 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -3,6 +3,7 @@
 
     COMMENT = Biology
 
+    SUBDIR += abyss
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile
new file mode 100644
index 000000000000..fa2ba2f9fabb
--- /dev/null
+++ b/biology/abyss/Makefile
@@ -0,0 +1,35 @@
+# $FreeBSD$
+
+PORTNAME=	abyss
+DISTVERSION=	2.1.5
+CATEGORIES=	biology
+MASTER_SITES=	http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Assembly By Short Sequences: parallel, paired-end sequence assembler
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \
+		ghc:lang/ghc \
+		pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer
+LIB_DEPENDS=	libffi.so:devel/libffi \
+		libgmp.so:math/gmp \
+		libomp.so:devel/openmp
+RUN_DEPENDS=	bash:shells/bash \
+		gmake:devel/gmake
+
+USES=		gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
+SHEBANG_FILES=	bin/${PORTNAME}-*
+SHEBANG_LANG=	make
+make_OLD_CMD=	/usr/bin/make
+make_CMD=	${PREFIX}/bin/gmake
+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>
diff --git a/biology/abyss/distinfo b/biology/abyss/distinfo
new file mode 100644
index 000000000000..1e1588ec91ed
--- /dev/null
+++ b/biology/abyss/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1551061546
+SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757
+SIZE (abyss-2.1.5.tar.gz) = 1201318
diff --git a/biology/abyss/files/patch-Common_Timer.h b/biology/abyss/files/patch-Common_Timer.h
new file mode 100644
index 000000000000..134b35c1e848
--- /dev/null
+++ b/biology/abyss/files/patch-Common_Timer.h
@@ -0,0 +1,11 @@
+--- Common/Timer.h.orig	2019-02-25 02:35:12 UTC
++++ Common/Timer.h
+@@ -3,6 +3,8 @@
+ 
+ #include <string>
+ 
++#include <time.h>
++
+ /**
+  * Time the duration between the construction and destruction of this
+  * timer object and log that duration.
diff --git a/biology/abyss/pkg-descr b/biology/abyss/pkg-descr
new file mode 100644
index 000000000000..77140fda19ac
--- /dev/null
+++ b/biology/abyss/pkg-descr
@@ -0,0 +1,6 @@
+ABySS is a de novo, parallel, paired-end sequence assembler that is designed for
+short reads. The single-processor version is useful for assembling genomes up to
+100 Mbases in size. The parallel version is implemented using MPI and is capable
+of assembling larger genomes.
+
+WWW: http://www.bcgsc.ca/platform/bioinfo/software/abyss
diff --git a/biology/abyss/pkg-plist b/biology/abyss/pkg-plist
new file mode 100644
index 000000000000..94ec1d8d98df
--- /dev/null
+++ b/biology/abyss/pkg-plist
@@ -0,0 +1,60 @@
+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