mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-19 00:13:33 +00:00
53 lines
1.4 KiB
Makefile
53 lines
1.4 KiB
Makefile
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>
|