diff --git a/biology/star/Makefile b/biology/star/Makefile index fc32ddebc58b..dd8137dee91f 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,47 +1,50 @@ PORTNAME= STAR -DISTVERSION= 2.7.10b +DISTVERSION= 2.7.11a 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 WRKSRC_SUBDIR= source MAKE_FLAGS= HTSLIB='' PLIST_FILES= bin/STAR post-patch: ${RM} -rf ${WRKSRC}/htslib ${REINPLACE_CMD} \ -e 's|"htslib/htslib/sam.h"||g' \ -e 's|"htslib/htslib/kstring.h"||g' \ -e 's|"htslib/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 diff --git a/biology/star/distinfo b/biology/star/distinfo index 6f7048071c63..395c98a981c1 100644 --- a/biology/star/distinfo +++ b/biology/star/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1689939622 -SHA256 (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5 -SIZE (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 12443703 +TIMESTAMP = 1692285897 +SHA256 (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a +SIZE (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 12463429 diff --git a/biology/star/files/patch-SpliceGraph.cpp b/biology/star/files/patch-SpliceGraph.cpp deleted file mode 100644 index b839bfe7e802..000000000000 --- a/biology/star/files/patch-SpliceGraph.cpp +++ /dev/null @@ -1,10 +0,0 @@ ---- SpliceGraph.cpp.orig 2023-07-21 15:27:26 UTC -+++ SpliceGraph.cpp -@@ -1,7 +1,6 @@ - /* - * Created by Fahimeh Mirhaj on 6/10/19. - */ --using namespace std; - - #include "SpliceGraph.h" - #include "GTF.h" diff --git a/biology/star/files/patch-opal_opal.cpp b/biology/star/files/patch-opal_opal.cpp deleted file mode 100644 index dcda064df27a..000000000000 --- a/biology/star/files/patch-opal_opal.cpp +++ /dev/null @@ -1,13 +0,0 @@ ---- opal/opal.cpp.orig 2021-11-26 16:14:46 UTC -+++ opal/opal.cpp -@@ -5,10 +5,8 @@ - #include - #include - --extern "C" { - #define SIMDE_ENABLE_NATIVE_ALIASES - #include // AVX2 and lower --} - - #include "opal.h" -