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biology/bowtie2: Update to 2.5.0

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Performance improvements and minor improvements
Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2022-11-04 18:47:34 -05:00
parent a6e687526d
commit f2f8bd75c4
3 changed files with 12 additions and 8 deletions
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2
biology/bowtie2/Makefile
View file

@ -1,6 +1,6 @@
PORTNAME= bowtie2
DISTVERSIONPREFIX= v
DISTVERSION= 2.4.5
DISTVERSION= 2.5.0
CATEGORIES= biology perl5 python
MAINTAINER= jwb@FreeBSD.org

6
biology/bowtie2/distinfo
View file

@ -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

12
biology/bowtie2/files/patch-Makefile
View file

@ -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