git: 1effaacbafd7 - main - biology/bowtie2: Update to 2.4.3

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef

commit 1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-05-17 23:40:15 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-05-17 23:40:15 +0000

    biology/bowtie2: Update to 2.4.3
    
    Drop tbb dependency (upstream switched to C++ threads)
    Add support for powerpc64
    
    Reported by:    portscout
    Tested by:      pkubaj (powerpc64*)
---
 biology/bowtie2/Makefile             | 11 +++------
 biology/bowtie2/distinfo             | 10 ++++----
 biology/bowtie2/files/patch-Makefile | 48 +++++++++++++-----------------------
 3 files changed, 26 insertions(+), 43 deletions(-)

diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index 2cd89b18642b..572338c8d90b 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.4.2
-PORTREVISION=		4
+DISTVERSION=		2.4.3
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb at FreeBSD.org
@@ -10,10 +9,8 @@ COMMENT=	Ultrafast, memory-efficient short read aligner
 LICENSE=	GPLv3+
 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=	aarch64 amd64 powerpc64le
-LIB_DEPENDS=	libtbb.so:devel/onetbb
+# Requires a 64-bit processor and depends on hard-coded asm instructions
+ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64 powerpc64le
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		gmake localbase:ldflags perl5 python shebangfix
@@ -23,7 +20,7 @@ USE_GITHUB=	yes
 SHEBANG_FILES=	bowtie2 bowtie2-build bowtie2-inspect \
 		scripts/bowtie2-hbb.sh scripts/*.pl
 GH_ACCOUNT=	BenLangmead
-GH_TUPLE=	nemequ:simde:422ed9c:simde
+GH_TUPLE=	simd-everywhere:simde-no-tests:f6a0b3b:simde
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index 57c4443eb8df..1671f9bf5b3d 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1618499065
-SHA256 (BenLangmead-bowtie2-v2.4.2_GH0.tar.gz) = ea33a1562faf759b21b3a905e20b87a3524ac4e53af8cd723d9a9f31ee159c8a
-SIZE (BenLangmead-bowtie2-v2.4.2_GH0.tar.gz) = 10590144
-SHA256 (nemequ-simde-422ed9c_GH0.tar.gz) = 3e7e962b499212cdddcaeca973d1c15d71a4b620afb46113d936ce5c3a8236ba
-SIZE (nemequ-simde-422ed9c_GH0.tar.gz) = 332230
+TIMESTAMP = 1621280053
+SHA256 (BenLangmead-bowtie2-v2.4.3_GH0.tar.gz) = 616017bcc68fc178418575fe39ffde42fff811d0d071bac7b1e7650288e4d166
+SIZE (BenLangmead-bowtie2-v2.4.3_GH0.tar.gz) = 10582150
+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 f082b4abb0d3..fb68d5913e52 100644
--- a/biology/bowtie2/files/patch-Makefile
+++ b/biology/bowtie2/files/patch-Makefile
@@ -1,39 +1,25 @@
---- Makefile.orig	2020-10-06 03:46:41 UTC
+--- Makefile.orig	2021-05-15 20:10:26 UTC
 +++ Makefile
-@@ -24,7 +24,7 @@
- PREFIX := /usr/local
- bindir := $(PREFIX)/bin
+@@ -32,7 +32,7 @@ BOWTIE_SHARED_MEM :=
  
--ARCH := $(shell uname -m)
-+ARCH := $(shell uname -p)
- LDLIBS := -lz
- GCC_PREFIX := $(shell dirname `which gcc`)
- GCC_SUFFIX :=
-@@ -201,22 +201,22 @@ endif
+ CXXFLAGS += -std=c++11
+ 
+-ARCH = $(shell uname -m)
++ARCH = $(shell uname -p)
+ NGS_VER ?= 2.9.2
+ VDB_VER ?= 2.9.2-1
+ 
+@@ -59,11 +59,11 @@ ifneq (,$(findstring Darwin,$(shell uname)))
+ endif
  
  BITS := 32
- SSE_FLAG := -msse2
--ifeq (x86_64,$(shell uname -m))
-+ifeq (x86_64,$(shell uname -p))
-   BITS := 64
--else ifeq (amd64,$(shell uname -m))
-+else ifeq (amd64,$(shell uname -p))
+-ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
++ifneq (,$(findstring $(shell uname -p), x86_64 amd64))
    BITS := 64
--else ifeq (aarch64,$(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 (powerpc64le,$(shell uname -p))
+   SSE_FLAG := -msse2
+   POPCNT_CAPABILITY ?= 1
+-else ifneq (,$(findstring $(shell uname -m), aarch64 arm64 s390x ppc64 ppc64le))
++else ifneq (,$(findstring $(shell uname -p), aarch64 arm64 s390x powerpc64 powerpc64le))
    BITS := 64
    SSE_FLAG :=
    CXXFLAGS += -fopenmp-simd