| Server IP : 82.208.35.60 / Your IP : 216.73.216.89 Web Server : Apache/2.4.55 (FreeBSD) OpenSSL/1.1.1q-freebsd PHP/7.3.31 System : FreeBSD server7.d2m.cz 12.4-RELEASE-p9 FreeBSD 12.4-RELEASE-p9 GENERIC amd64 User : studiokobylisy_cz ( 1008) PHP Version : 7.3.31 Disable Function : NONE MySQL : OFF | cURL : ON | WGET : OFF | Perl : OFF | Python : OFF | Sudo : OFF | Pkexec : OFF Directory : /usr/ports/biology/star/ |
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PORTNAME= STAR
DISTVERSION= 2.7.9a
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= i386 powerpc
NOT_FOR_ARCHS_REASON=Needs 16+ GiB RAM for typical eukaryotic genome
.if !exists(/usr/include/omp.h)
BROKEN= requires OpenMP support that is missing on this architecture
.endif
LIB_DEPENDS= libhts.so:biology/htslib
USES= compiler:c++11-lang gmake localbase:ldflags
USE_GITHUB= yes
GH_ACCOUNT= alexdobin
WRKSRC_SUBDIR= source
MAKE_FLAGS= HTSLIB=''
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
.include <bsd.port.mk>