diff options
Diffstat (limited to 'biology/star/Makefile')
| -rw-r--r-- | biology/star/Makefile | 32 |
1 files changed, 28 insertions, 4 deletions
diff --git a/biology/star/Makefile b/biology/star/Makefile index 67da9de6c511..968caa762551 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,26 +1,50 @@ PORTNAME= STAR -DISTVERSION= 2.7.3a +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 -# 64-bit only, needs 16+ GiB RAM for typical eukaryotic genome -NOT_FOR_ARCHS= i386 powerpc +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 -USES= compiler:c++11-lang gmake +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 WRKSRC_SUBDIR= source +MAKE_FLAGS= HTSLIB='' CXXFLAGS_SIMD="" PLIST_FILES= bin/STAR +post-patch: + ${RM} -rf ${WRKSRC}/htslib + ${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 |