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PORTNAME= ncbi-vdb
DISTVERSION= 2.11.0
PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= mzaki@niid.go.jp
COMMENT= NCBI's virtualized back-end for accessing Sequence Read Archive
LICENSE= PD
LICENSE_FILE= ${WRKSRC}/LICENSE
ONLY_FOR_ARCHS= amd64 i386
ONLY_FOR_ARCHS_REASON= libs/search/nucstrstr.c requires SSE2 instructions
BUILD_DEPENDS= bash:shells/bash \
libepoll-shim>0:devel/libepoll-shim
LIB_DEPENDS= libxml2.so:textproc/libxml2 \
libhdf5.so:science/hdf5 \
libmbedtls.so:security/mbedtls
USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix
USE_PERL5= build
USE_LDCONFIG= yes
USE_GITHUB= yes
GH_ACCOUNT= ncbi
GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs # ported as biology/ngs-sdk
SHEBANG_GLOB= *.sh *.pl
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --with-xml2-prefix=${LOCALBASE} \
--with-hdf5-prefix=${LOCALBASE} \
--with-mbedtls-prefix=${LOCALBASE} \
CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
MAKE_ENV+= CPATH="${LOCALBASE}/include/libepoll-shim"
MAKE_ARGS+= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
CFLAGS+= -I${WRKSRC}/lib
MAKE_JOBS_UNSAFE= yes
post-extract:
@${LN} -sf ${WRKSRC_ngs} ${WRKDIR}/ngs
@${LN} -sf ${WRKSRC} ${WRKDIR}/${PORTNAME}
pre-patch:
@${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/
@for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done
@${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh
@${MKDIR} ${WRKSRC}/interfaces/os/bsd
@${CP} -p ${WRKSRC}/interfaces/os/mac/endian.h ${WRKSRC}/interfaces/os/bsd/
post-patch:
@${GREP} -q '@@PREFIX@@' ${WRKSRC}/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)
@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/libs/kfg/config.c
post-configure:
@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP
# The 'install' target installs broken-looking static libs with symlinks.
# This is intentional, see comments https://github.com/ncbi/ncbi-vdb/issues/36#issuecomment-817990790 This may change in future versions.
.include <bsd.port.mk>
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