diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile index 2b9eb8e674cb..5ee287444dc0 100644 --- a/biology/sra-tools/Makefile +++ b/biology/sra-tools/Makefile @@ -1,66 +1,67 @@ PORTNAME= sra-tools DISTVERSION= 3.0.6 +PORTREVISION= 1 CATEGORIES= biology java MAINTAINER= jwb@FreeBSD.org COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives WWW= https://github.com/ncbi/sra-tools LICENSE= PD LGPL21+ LICENSE_COMB= multi LICENSE_FILE_PD= ${WRKSRC}/LICENSE LICENSE_DISTFILES_LGPL21+ = # Untested on other platforms, aarch64 support was recently added upstream ONLY_FOR_ARCHS= aarch64 amd64 ONLY_FOR_ARCHS_REASON= Upstream explicitly supports specific platforms BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libxml2.so:textproc/libxml2 \ libhdf5.so:science/hdf5 \ libepoll-shim.so:devel/libepoll-shim \ libzstd.so:archivers/zstd USES= bison cmake shebangfix USE_GITHUB= yes USE_LDCONFIG= ${PREFIX}/lib64 USE_JAVA= yes # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present JAVA_VERSION= 17+ OPTIONS_DEFINE= EXAMPLES SHEBANG_GLOB= *.sh GH_ACCOUNT= ncbi GH_TUPLE+= ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb CMAKE_ARGS+= -DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib post-extract: @${MKDIR} ${WRKSRC}/ncbi-vdb/interfaces/os/bsd @${CP} ${FILESDIR}/*.h ${WRKSRC}/ncbi-vdb/interfaces/os/bsd # cd ${WRKDIR} && ${LN} -s ${WRKSRC}/ncbi-vdb . pre-configure: # This follows a static patch. Run "make clean patch" before # updating the patch. ${REINPLACE_CMD} -e 's|/usr/local/etc/ncbi|${PREFIX}/etc/ncbi|g' \ ${WRKSRC}/ncbi-vdb/libs/kfg/config.c ${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \ ${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make post-stage: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION} ${MV} ${STAGEDIR}${PREFIX}/share/examples ${STAGEDIR}${PREFIX}/share/examples-sratools ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${MV} ${STAGEDIR}${PREFIX}/share/examples-sratools/* ${STAGEDIR}${EXAMPLESDIR} ${RMDIR} ${STAGEDIR}${PREFIX}/share/examples-sratools ${MV} ${STAGEDIR}${PREFIX}/share/examples-java ${STAGEDIR}${EXAMPLESDIR}/java ${MV} ${STAGEDIR}${PREFIX}/share/examples-python ${STAGEDIR}${EXAMPLESDIR}/python post-stage-EXAMPLES-off: ${RM} -r ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist index 20e3af7ac25d..1976fb428463 100644 --- a/biology/sra-tools/pkg-plist +++ b/biology/sra-tools/pkg-plist @@ -1,282 +1,282 @@ bin/abi-dump bin/abi-dump.3 bin/abi-dump.3.0.6 bin/align-info bin/align-info.3 bin/align-info.3.0.6 bin/cache-mgr bin/cache-mgr.3 bin/cache-mgr.3.0.6 bin/check-corrupt bin/check-corrupt.3 bin/check-corrupt.3.0.6 bin/fasterq-dump bin/fasterq-dump-orig.3.0.6 bin/fasterq-dump.3 bin/fasterq-dump.3.0.6 bin/fastq-dump bin/fastq-dump-orig.3.0.6 bin/fastq-dump.3 bin/fastq-dump.3.0.6 bin/illumina-dump bin/illumina-dump.3 bin/illumina-dump.3.0.6 bin/kdbmeta bin/kdbmeta.3 bin/kdbmeta.3.0.6 bin/ngs-pileup bin/ngs-pileup.3 bin/ngs-pileup.3.0.6 bin/prefetch bin/prefetch-orig.3.0.6 bin/prefetch.3 bin/prefetch.3.0.6 bin/rcexplain bin/rcexplain.3 bin/rcexplain.3.0.6 bin/ref-variation bin/ref-variation.3 bin/ref-variation.3.0.6 bin/sam-dump bin/sam-dump-orig.3.0.6 bin/sam-dump.3 bin/sam-dump.3.0.6 bin/sff-dump bin/sff-dump.3 bin/sff-dump.3.0.6 bin/sra-info bin/sra-info.3 bin/sra-info.3.0.6 bin/sra-pileup bin/sra-pileup-orig.3.0.6 bin/sra-pileup.3 bin/sra-pileup.3.0.6 bin/sra-search bin/sra-search.3 bin/sra-search.3.0.6 bin/sra-stat bin/sra-stat.3 bin/sra-stat.3.0.6 bin/srapath bin/srapath-orig.3.0.6 bin/srapath.3 bin/srapath.3.0.6 bin/sratools bin/sratools.3 bin/sratools.3.0.6 bin/test-sra bin/test-sra.3 bin/test-sra.3.0.6 bin/var-expand bin/var-expand.3 bin/var-expand.3.0.6 bin/vdb-config bin/vdb-config.3 bin/vdb-config.3.0.6 bin/vdb-decrypt bin/vdb-decrypt.3 bin/vdb-decrypt.3.0.6 bin/vdb-dump bin/vdb-dump-orig.3.0.6 bin/vdb-dump.3 bin/vdb-dump.3.0.6 bin/vdb-encrypt bin/vdb-encrypt.3 bin/vdb-encrypt.3.0.6 bin/vdb-validate bin/vdb-validate.3 bin/vdb-validate.3.0.6 include/ncbi-vdb/NGS.hpp include/ngs/Alignment.hpp include/ngs/AlignmentIterator.hpp include/ngs/ErrorMsg.hpp include/ngs/Fragment.hpp include/ngs/FragmentIterator.hpp include/ngs/Package.hpp include/ngs/Pileup.hpp include/ngs/PileupEvent.hpp include/ngs/PileupEventIterator.hpp include/ngs/PileupIterator.hpp include/ngs/Read.hpp include/ngs/ReadCollection.hpp include/ngs/ReadGroup.hpp include/ngs/ReadGroupIterator.hpp include/ngs/ReadIterator.hpp include/ngs/Reference.hpp include/ngs/ReferenceIterator.hpp include/ngs/ReferenceSequence.hpp include/ngs/Statistics.hpp include/ngs/StringRef.hpp include/ngs/adapter/AlignmentItf.hpp include/ngs/adapter/ErrorMsg.hpp include/ngs/adapter/FragmentItf.hpp include/ngs/adapter/PileupEventItf.hpp include/ngs/adapter/PileupItf.hpp include/ngs/adapter/ReadCollectionItf.hpp include/ngs/adapter/ReadGroupItf.hpp include/ngs/adapter/ReadItf.hpp include/ngs/adapter/Refcount.hpp include/ngs/adapter/ReferenceItf.hpp include/ngs/adapter/ReferenceSequenceItf.hpp include/ngs/adapter/StatisticsItf.hpp include/ngs/adapter/StringItf.hpp include/ngs/adapter/defs.h include/ngs/inl/Alignment.hpp include/ngs/inl/AlignmentIterator.hpp include/ngs/inl/Fragment.hpp include/ngs/inl/FragmentIterator.hpp include/ngs/inl/Package.hpp include/ngs/inl/Pileup.hpp include/ngs/inl/PileupEvent.hpp include/ngs/inl/PileupEventIterator.hpp include/ngs/inl/PileupIterator.hpp include/ngs/inl/Read.hpp include/ngs/inl/ReadCollection.hpp include/ngs/inl/ReadGroup.hpp include/ngs/inl/ReadGroupIterator.hpp include/ngs/inl/ReadIterator.hpp include/ngs/inl/Reference.hpp include/ngs/inl/ReferenceIterator.hpp include/ngs/inl/ReferenceSequence.hpp include/ngs/inl/Statistics.hpp include/ngs/inl/StringRef.hpp include/ngs/itf/AlignmentItf.h include/ngs/itf/AlignmentItf.hpp include/ngs/itf/ErrBlock.h include/ngs/itf/ErrBlock.hpp include/ngs/itf/ErrorMsg.hpp include/ngs/itf/FragmentItf.h include/ngs/itf/FragmentItf.hpp include/ngs/itf/PackageItf.hpp include/ngs/itf/PileupEventItf.h include/ngs/itf/PileupEventItf.hpp include/ngs/itf/PileupItf.h include/ngs/itf/PileupItf.hpp include/ngs/itf/ReadCollectionItf.h include/ngs/itf/ReadCollectionItf.hpp include/ngs/itf/ReadGroupItf.h include/ngs/itf/ReadGroupItf.hpp include/ngs/itf/ReadItf.h include/ngs/itf/ReadItf.hpp include/ngs/itf/Refcount.h include/ngs/itf/Refcount.hpp include/ngs/itf/ReferenceItf.h include/ngs/itf/ReferenceItf.hpp include/ngs/itf/ReferenceSequenceItf.h include/ngs/itf/ReferenceSequenceItf.hpp include/ngs/itf/StatisticsItf.h include/ngs/itf/StatisticsItf.hpp include/ngs/itf/StringItf.h include/ngs/itf/StringItf.hpp include/ngs/itf/VTable.h include/ngs/itf/VTable.hpp include/ngs/itf/defs.h include/ngs/unix/arm64/atomic32.h include/ngs/unix/fat86/atomic32.h include/ngs/unix/i386/atomic32.h include/ngs/unix/x86_64/atomic32.h include/ngs/win/atomic32.h include/ngs/win/stdbool.h jar/ngs-doc.jar jar/ngs-examples.jar jar/ngs-java.jar jar/ngs-src.jar lib64/libncbi-ngs-c++-static.a lib64/libncbi-ngs-c++.a lib64/libncbi-ngs-c++.a.3 lib64/libncbi-ngs-c++.a.3.0.6 lib64/libncbi-ngs-static.a lib64/libncbi-ngs.a lib64/libncbi-ngs.a.3 lib64/libncbi-ngs.a.3.0.6 lib64/libncbi-ngs.so lib64/libncbi-ngs.so.3 lib64/libncbi-ngs.so.3.0.6 lib64/libngs-c++-static.a lib64/libngs-c++.a lib64/libngs-c++.a.3 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