biology/bowtie2: Update to 2.5.0

Performance improvements and minor improvements Changes: https://github.com/BenLangmead/bowtie2/tags Reported by: portscout
freebsd · Nov 4, 2022 · f2f8bd7 · f2f8bd7
1 parent a6e6875
commit f2f8bd7
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Showing 3 changed files with 12 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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