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Code Issues Releases Activity

biology/bowtie2: Upgrade to 2.4.1

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Numerous bugfixes and enhancements
Enable experimental support for aarch64

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2020-03-01 16:01:12 +00:00
parent 622922e74c
commit c37fa58a73
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=527560
3 changed files with 30 additions and 53 deletions
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5
biology/bowtie2/Makefile
View File

@ -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

6
biology/bowtie2/distinfo
View File

@ -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

72
biology/bowtie2/files/patch-Makefile
View File

@ -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