diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2020-03-01 16:01:12 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2020-03-01 16:01:12 +0000 |
| commit | c37fa58a73920b0b01f414a8ea5d7acd0ff6c441 (patch) | |
| tree | 1692e5851360544a509648c79e7a178ded304884 /biology | |
| parent | 622922e74c957ab35af7a6e795d3adc16859d448 (diff) | |
| download | ports-c37fa58a73920b0b01f414a8ea5d7acd0ff6c441.tar.gz ports-c37fa58a73920b0b01f414a8ea5d7acd0ff6c441.zip | |
biology/bowtie2: Upgrade to 2.4.1
Numerous bugfixes and enhancements
Enable experimental support for aarch64
Reported by: portscout
Notes
Notes:
svn path=/head/; revision=527560
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bowtie2/Makefile | 5 | ||||
| -rw-r--r-- | biology/bowtie2/distinfo | 6 | ||||
| -rw-r--r-- | biology/bowtie2/files/patch-Makefile | 72 |
3 files changed, 30 insertions, 53 deletions
diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index 09b922fdcb67..df031164588d 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -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 diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo index 08c9e69bacfd..da64a3e3c0f3 100644 --- a/biology/bowtie2/distinfo +++ b/biology/bowtie2/distinfo @@ -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 diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile index 8312e59dc84d..85d870c135cc 100644 --- a/biology/bowtie2/files/patch-Makefile +++ b/biology/bowtie2/files/patch-Makefile @@ -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 - # - --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 := $(shell cat VERSION) +@@ -200,22 +200,22 @@ endif BITS := 32 + SSE_FLAG := -msse2 -ifeq (x86_64,$(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 |