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