git: 65ce3f1684bc - main - biology/bowtie2: Update to 2.5.1

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=65ce3f1684bc6a0457bfc55feb059baf76bbee2a

commit 65ce3f1684bc6a0457bfc55feb059baf76bbee2a
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-01-21 22:30:48 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-01-21 22:30:48 +0000

    biology/bowtie2: Update to 2.5.1
    
    A few minor fixes and enhancements
    
    Changes:    https://github.com/BenLangmead/bowtie2/tags
    
    Reported by:    portscout
---
 biology/bowtie2/Makefile             |  2 +-
 biology/bowtie2/distinfo             |  6 +++---
 biology/bowtie2/files/patch-Makefile | 28 +++++-----------------------
 3 files changed, 9 insertions(+), 27 deletions(-)

diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index b227373a69b0..14777fb43760 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.5.0
+DISTVERSION=		2.5.1
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index 1ebf87291129..69c8b6900f9a 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1667400686
-SHA256 (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 55dedeba8bea240d3ce3f46211d6e14310035c1de5a3e9ac33f72f739165fea0
-SIZE (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 10598633
+TIMESTAMP = 1674338476
+SHA256 (BenLangmead-bowtie2-v2.5.1_GH0.tar.gz) = 3fe00f4f89b5dd85fd9317e2168ec93f30dbb75d7950a08516c767d21eca7c27
+SIZE (BenLangmead-bowtie2-v2.5.1_GH0.tar.gz) = 10598627
 SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8
 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743
diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile
index 23bb0fae0c58..abbe01f5f982 100644
--- a/biology/bowtie2/files/patch-Makefile
+++ b/biology/bowtie2/files/patch-Makefile
@@ -1,29 +1,11 @@
---- Makefile.orig	2022-11-01 01:53:08 UTC
+--- Makefile.orig	2023-01-21 21:59:18 UTC
 +++ Makefile
-@@ -32,7 +32,7 @@ BOWTIE_SHARED_MEM :=
- 
- CXXFLAGS += -std=c++11
- 
--ARCH = $(shell uname -m)
-+ARCH = $(shell uname -p)
- NGS_VER ?= 2.9.2
- VDB_VER ?= 2.9.2-1
- 
-@@ -62,7 +62,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
+@@ -61,7 +61,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
  endif
  
  BITS := 32
--ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
-+ifneq (,$(findstring $(shell uname -p), x86_64 amd64))
+-ARCH ?= $(shell uname -m)
++ARCH ?= $(shell uname -p)
+ ifneq (,$(findstring $(ARCH), x86_64 amd64))
    BITS := 64
    ifeq (1, $(SSE_AVX2))
- 	SSE_FLAG := -mavx2 -faligned-new -DSSE_AVX2
-@@ -71,7 +71,7 @@ ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
-   endif
- 
-   POPCNT_CAPABILITY ?= 1
--else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le))
-+else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x powerpc64 powerpc64le ppc64 ppc64le))
-   BITS := 64
-   SSE_FLAG :=
-   CXXFLAGS += -fopenmp-simd