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PORTNAME= sra-tools
DISTVERSION= 2.11.0
PORTREVISION= 2
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives
LICENSE= PD LGPL21+
LICENSE_COMB= multi
LICENSE_FILE_PD= ${WRKSRC}/LICENSE
LICENSE_DISTFILES_LGPL21+ =
ONLY_FOR_ARCHS= amd64
ONLY_FOR_ARCHS_REASON= NCBI-VDB requires SSE2 instructions, no 32-bit support
BUILD_DEPENDS= bash:shells/bash \
${LOCALBASE}/lib/libngs-c++.a:biology/ngs-sdk
LIB_DEPENDS= libxml2.so:textproc/libxml2 \
libhdf5.so:science/hdf5 \
libepoll-shim.so:devel/libepoll-shim
USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix
USE_PERL5= build
USE_GITHUB= yes
SHEBANG_GLOB= *.sh *.pl
GH_ACCOUNT= ncbi
GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs/ngs # ported as biology/ngs-sdk
GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --with-ngs-sdk-prefix=${LOCALBASE} \
--with-ncbi-vdb-sources=${NCBI_VDB_WRKSRC} \
--with-xml2-prefix=${LOCALBASE} \
--with-hdf5-prefix=${LOCALBASE} \
CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" \
--with-ncbi-vdb-build=${NCBI_VDB_WRKSRC}/amd64-portbld-freebsd$$(${FREEBSD_RELEASE})
MAKE_ARGS= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" \
INST_ETCDIR=${STAGEDIR}${PREFIX}/etc
NCBI_VDB_WRKSRC= ${WRKSRC}/ncbi-vdb
NCBI_VDB_FILESDIR= ${FILESDIR}
FREEBSD_RELEASE= uname -r | cut -d - -f 1
CFLAGS+= -I${WRKSRC}/interfaces/os/sun
CXXFLAGS+= -I${WRKSRC}/interfaces/os/sun
CONFLICTS_INSTALL= kget
BINARY_ALIAS= gcc=${CC} g++=${CXX}
# for port developers, building with these options may fail
OPTIONS_DEFINE= DEBUG OPTIMIZED_CFLAGS TEST
DEBUG_PREVENTS= OPTIMIZED_CFLAGS
DEBUG_CONFIGURE_WITH= debug
OPTIMIZED_CFLAGS_MAKE_ARGS_OFF= OPT=""
TEST_TEST_TARGET= test
TEST_USES= python
# ncbi-vdb build extras
VDB_CONFIGURE_ARGS= \
--with-xml2-prefix=${LOCALBASE} \
--with-hdf5-prefix=${LOCALBASE} \
--prefix=${PREFIX} \
--build=amd64-portbld-freebsd$$(${FREEBSD_RELEASE}) \
CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}"
VDB_MAKE_ARGS+= -j 1 CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}"
MAKE_ENV+= CPATH="${LOCALBASE}/include/libepoll-shim"
CFLAGS+= -I${WRKSRC}/lib
pre-patch:
@${CP} ${FILESDIR}/Makefile.bsd ${NCBI_VDB_WRKSRC}/build/
@${CP} ${FILESDIR}/ld.bsd.*.sh ${NCBI_VDB_WRKSRC}/build/
@${MKDIR} ${NCBI_VDB_WRKSRC}/interfaces/os/bsd
@${CP} -p ${NCBI_VDB_WRKSRC}/interfaces/os/mac/endian.h \
${NCBI_VDB_WRKSRC}/interfaces/os/bsd/
post-patch:
@${GREP} -q '@@PREFIX@@' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1)
@${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/ncbi-vdb/libs/kfg/config.c
@${LN} -s ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64 ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/amd64
post-patch-TEST-on:
@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|' ${WRKSRC}/test/kget/Makefile
pre-configure:
@${CP} ${NCBI_VDB_WRKSRC}/setup/os-arch.prl ${WRKSRC}/setup/os-arch.prl
# same as in biology/ncbi-vdb
@${CP} ${NCBI_VDB_FILESDIR}/Makefile.bsd ${WRKSRC}/build/
@${CP} ${NCBI_VDB_WRKSRC}/build/ld.bsd.*.sh ${WRKSRC}/build/
@${MKDIR} ${WRKSRC}/interfaces/override
@${CP} ${NCBI_VDB_WRKSRC}/interfaces/os/sun/atomic32.h ${WRKSRC}/interfaces/override
@${CP} ${FILESDIR}/byteswap.h ${WRKSRC}/interfaces/override
@cd ${WRKSRC}/ncbi-vdb && ./configure ${VDB_CONFIGURE_ARGS}
@${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/ncbi-vdb/build/COMP
@cd ${WRKSRC}/ncbi-vdb && ${DO_MAKE_BUILD} ${VDB_MAKE_ARGS}
post-build-TEST-on: do-test
do-install:
cd ${WRKSRC}/amd64-portbld-freebsd*/sra-tools/bsd/clang/*/rel/bin && \
for f in `ls *.${PORTVERSION}`; do \
${INSTALL_PROGRAM} $${f} \
${STAGEDIR}${PREFIX}/bin/`basename $${f%%.${PORTVERSION}}`; \
done
.include <bsd.port.mk>
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