mirror of https://git.FreeBSD.org/ports.git
53 lines
1.4 KiB
Makefile
53 lines
1.4 KiB
Makefile
PORTNAME= STAR
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DISTVERSION= 2.7.11a
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PORTREVISION= 1
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CATEGORIES= biology
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PKGNAMEPREFIX= rna-
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Spliced Transcripts Alignment to a Reference
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WWW= https://github.com/alexdobin/STAR
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LICENSE= GPLv3
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LICENSE_FILE= ${WRKDIR}/STAR-${DISTVERSION}/LICENSE
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NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc powerpcspe
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NOT_FOR_ARCHS_REASON= Requires 64-bit processor
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.if !exists(/usr/include/omp.h)
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BROKEN= requires OpenMP support that is missing on this architecture
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.endif
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BUILD_DEPENDS= xxd:sysutils/xxd
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LIB_DEPENDS= libhts.so:biology/htslib
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USES= compiler:c++11-lang gmake localbase:ldflags
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# FIXME: When built with clang, number of input reads = 0
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USE_GCC= yes
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USE_GITHUB= yes
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GH_ACCOUNT= alexdobin
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EXTRACT_AFTER_ARGS= --exclude ${GH_PROJECT_DEFAULT}-${GH_TAGNAME_EXTRACT}/source/htslib --no-same-owner --no-same-permissions
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WRKSRC_SUBDIR= source
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MAKE_FLAGS= HTSLIB='' CXXFLAGS_SIMD=""
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PLIST_FILES= bin/STAR
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post-patch:
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${REINPLACE_CMD} \
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-e 's|"htslib/htslib/sam.h"|<htslib/sam.h>|g' \
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-e 's|"htslib/htslib/kstring.h"|<htslib/kstring.h>|g' \
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-e 's|"htslib/htslib/bgzf.h"|<htslib/bgzf.h>|g' \
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${WRKSRC}/BAMfunctions.cpp \
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${WRKSRC}/IncludeDefine.h \
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${WRKSRC}/STAR.cpp \
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${WRKSRC}/bamRemoveDuplicates.cpp \
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${WRKSRC}/bam_cat.c \
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${WRKSRC}/bam_cat.h \
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${WRKSRC}/signalFromBAM.h
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/STAR ${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.mk>
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