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# $FreeBSD$
PORTNAME= abyss
DISTVERSION= 2.1.5
PORTREVISION= 4
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}-*
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>
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