Date: Sun, 1 Mar 2020 16:01:12 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r527560 - in head/biology/bowtie2: . files Message-ID: <202003011601.021G1Cb4022112@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: jwb Date: Sun Mar 1 16:01:12 2020 New Revision: 527560 URL: https://svnweb.freebsd.org/changeset/ports/527560 Log: biology/bowtie2: Upgrade to 2.4.1 Numerous bugfixes and enhancements Enable experimental support for aarch64 Reported by: portscout Modified: head/biology/bowtie2/Makefile head/biology/bowtie2/distinfo head/biology/bowtie2/files/patch-Makefile Modified: head/biology/bowtie2/Makefile ============================================================================== --- head/biology/bowtie2/Makefile Sun Mar 1 16:00:12 2020 (r527559) +++ head/biology/bowtie2/Makefile Sun Mar 1 16:01:12 2020 (r527560) @@ -2,8 +2,7 @@ PORTNAME= bowtie2 DISTVERSIONPREFIX= v -DISTVERSION= 2.3.5.1 -PORTREVISION= 2 +DISTVERSION= 2.4.1 CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org @@ -14,7 +13,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE # Requires a 64-bit processor and depends on hard-coded SSE instructions # Experimental support for AARCH64 as of 2.3.5 -ONLY_FOR_ARCHS= amd64 +ONLY_FOR_ARCHS= aarch64 amd64 LIB_DEPENDS= libtbb.so:devel/tbb RUN_DEPENDS= bash:shells/bash Modified: head/biology/bowtie2/distinfo ============================================================================== --- head/biology/bowtie2/distinfo Sun Mar 1 16:00:12 2020 (r527559) +++ head/biology/bowtie2/distinfo Sun Mar 1 16:01:12 2020 (r527560) @@ -1,3 +1,3 @@ -TIMESTAMP = 1555781941 -SHA256 (BenLangmead-bowtie2-v2.3.5.1_GH0.tar.gz) = 86a018af1090900c160a0990cc106569805aa64a3ec8708e1d2127839e4a94b4 -SIZE (BenLangmead-bowtie2-v2.3.5.1_GH0.tar.gz) = 10587039 +TIMESTAMP = 1583075948 +SHA256 (BenLangmead-bowtie2-v2.4.1_GH0.tar.gz) = 9fb25513886bf294217dd9c5ca26d18dd5e02e0ae999935ac7ba5700befc492e +SIZE (BenLangmead-bowtie2-v2.4.1_GH0.tar.gz) = 10588621 Modified: head/biology/bowtie2/files/patch-Makefile ============================================================================== --- head/biology/bowtie2/files/patch-Makefile Sun Mar 1 16:00:12 2020 (r527559) +++ head/biology/bowtie2/files/patch-Makefile Sun Mar 1 16:01:12 2020 (r527560) @@ -1,52 +1,30 @@ ---- Makefile.orig 2019-04-17 02:40:25 UTC +--- Makefile.orig 2020-03-01 15:16:08 UTC +++ Makefile -@@ -21,8 +21,9 @@ - # Makefile for bowtie, bowtie2-build, bowtie2-inspect - # +@@ -200,22 +200,22 @@ endif --prefix := /usr/local --bindir := $(prefix)/bin -+# Use PREFIX (upper case) provided by many package managers -+PREFIX ?= /usr/local -+bindir := $(PREFIX)/bin - - LDLIBS := -lz - GCC_PREFIX := $(shell dirname `which gcc`) -@@ -30,8 +31,9 @@ GCC_SUFFIX := - CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) - CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) - CXX ?= $(CPP) --CXXFLAGS += -std=c++98 --ifeq (aarch64,$(shell uname -m)) -+# long long is unsupported in c++98 -+# CXXFLAGS += -std=c++98 -+ifeq (aarch64,$(shell uname -p)) - CXXFLAGS += -fopenmp-simd - CPPFLAGS += -Ithird_party/simde - endif -@@ -198,13 +200,13 @@ SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c) - VERSION := $(shell cat VERSION) - BITS := 32 + SSE_FLAG := -msse2 -ifeq (x86_64,$(shell uname -m)) +ifeq (x86_64,$(shell uname -p)) - BITS := 64 - endif --ifeq (amd64,$(shell uname -m)) -+ifeq (amd64,$(shell uname -p)) - BITS := 64 - endif --ifeq (aarch64,$(shell uname -m)) -+ifeq (aarch64,$(shell uname -p)) - BITS := 64 - endif - # msys will always be 32 bit so look at the cpu arch instead. -@@ -219,7 +221,7 @@ endif - - SSE_FLAG := -msse2 - M64_FLAG := -m64 --ifeq (aarch64,$(shell uname -m)) -+ifeq (aarch64,$(shell uname -p)) - SSE_FLAG = - M64_FLAG = - endif + BITS := 64 +-else ifeq (amd64,$(shell uname -m)) ++else ifeq (amd64,$(shell uname -p)) + BITS := 64 +-else ifeq (aarch64,$(shell uname -m)) ++else ifeq (aarch64,$(shell uname -p)) + BITS := 64 + SSE_FLAG := + CXXFLAGS := -fopenmp-simd + CPPFLAGS := -Ithird_party/simde +-else ifeq (s390x,$(shell uname -m)) ++else ifeq (s390x,$(shell uname -p)) + BITS := 64 + SSE_FLAG := + CXXFLAGS := -fopenmp-simd + CPPFLAGS := -Ithird_party/simde + SANITIZER_FLAGS := +-else ifeq (ppc64le,$(shell uname -m)) ++else ifeq (ppc64le,$(shell uname -p)) + BITS := 64 + SSE_FLAG := + CXXFLAGS := -fopenmp-simd
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202003011601.021G1Cb4022112>