git: f2f8bd75c4ac - main - biology/bowtie2: Update to 2.5.0

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Fri, 04 Nov 2022 23:49:03 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa

commit f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-11-04 23:47:34 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-11-04 23:49:02 +0000

    biology/bowtie2: Update to 2.5.0
    
    Performance improvements and minor improvements
    Changes:    https://github.com/BenLangmead/bowtie2/tags
    
    Reported by:    portscout
---
 biology/bowtie2/Makefile             |  2 +-
 biology/bowtie2/distinfo             |  6 +++---
 biology/bowtie2/files/patch-Makefile | 12 ++++++++----
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index 6ca11a69916f..b227373a69b0 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.4.5
+DISTVERSION=		2.5.0
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index afe87ffa42f1..1ebf87291129 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1642699775
-SHA256 (BenLangmead-bowtie2-v2.4.5_GH0.tar.gz) = db101391b54a5e0eeed7469b05aee55ee6299558b38607f592f6b35a7d41dcb6
-SIZE (BenLangmead-bowtie2-v2.4.5_GH0.tar.gz) = 10585723
+TIMESTAMP = 1667400686
+SHA256 (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 55dedeba8bea240d3ce3f46211d6e14310035c1de5a3e9ac33f72f739165fea0
+SIZE (BenLangmead-bowtie2-v2.5.0_GH0.tar.gz) = 10598633
 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 fb68d5913e52..491fd10e7b79 100644
--- a/biology/bowtie2/files/patch-Makefile
+++ b/biology/bowtie2/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig	2021-05-15 20:10:26 UTC
+--- Makefile.orig	2022-11-02 14:50:38 UTC
 +++ Makefile
 @@ -32,7 +32,7 @@ BOWTIE_SHARED_MEM :=
  
@@ -9,17 +9,21 @@
  NGS_VER ?= 2.9.2
  VDB_VER ?= 2.9.2-1
  
-@@ -59,11 +59,11 @@ ifneq (,$(findstring Darwin,$(shell uname)))
+@@ -62,7 +62,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
  endif
  
  BITS := 32
 -ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
 +ifneq (,$(findstring $(shell uname -p), x86_64 amd64))
    BITS := 64
-   SSE_FLAG := -msse2
+   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 $(shell uname -p), aarch64 arm64 s390x powerpc64 powerpc64le))
++else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x ppc64 ppc64le))
    BITS := 64
    SSE_FLAG :=
    CXXFLAGS += -fopenmp-simd