svn commit: r527560 - in head/biology/bowtie2: . files

[Jason W. Bacon]

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 at 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