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PORTNAME= abyss
DISTVERSION= 2.3.7
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler
WWW= https://www.bcgsc.ca/resources/software/abyss
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/LICENSE
BROKEN_i386= result of comparison of constant 18446744073709551615 with expression of type 'size_t', see https://github.com/bcgsc/abyss/issues/310
BUILD_DEPENDS= ${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \
ghc:lang/ghc \
pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer
LIB_DEPENDS= libbtllib.so:biology/btllib \
libffi.so:devel/libffi \
libgmp.so:math/gmp \
libmpich.so:net/mpich # binaries aren't linked with libmpich.so for some reason
RUN_DEPENDS= bash:shells/bash \
gmake:devel/gmake
USES= autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite
USE_GITHUB= yes
GH_ACCOUNT= bcgsc
SHEBANG_FILES= bin/${PORTNAME}-* DataBase/abyss-db-txt
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
TEST_TARGET= check # tests fail to compile, see https://github.com/bcgsc/abyss/issues/453
OPTIONS_DEFINE= DOCS
PORTDOCS= *
PORTSCOUT= limit:^[0-9\.]*$$ # to ignore alpha-numeric tags
.include <bsd.port.pre.mk>
.if ${OPSYS} == FreeBSD && ( ${OSVERSION} >= 1400079 || ( ${OSVERSION} >= 1302505 && ${OSVERSION} < 1400000 ))
CFLAGS+= -Wno-error=unused-but-set-variable
.endif
.include <bsd.port.post.mk>
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