PORTNAME= abyss DISTVERSION= 2.3.10 CATEGORIES= biology MAINTAINER= [email protected] 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= ${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 PORTSCOUT= limit:^[0-9\.]*$$ # to ignore alpha-numeric tags PORTDOCS= * OPTIONS_DEFINE= DOCS TESTING_UNSAFE= yes # tests fail to compile, see https://github.com/bcgsc/abyss/issues/453 .include <bsd.port.pre.mk> .if ${OPSYS} == FreeBSD CFLAGS+= -Wno-error=unused-but-set-variable .endif .include <bsd.port.post.mk>
