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biology/bowtie2: Update to 2.5.1

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A few minor fixes and enhancements

Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2023-01-21 16:30:48 -06:00
parent b4a0643820
commit 65ce3f1684
3 changed files with 9 additions and 27 deletions
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2
biology/bowtie2/Makefile
View File

@ -1,6 +1,6 @@
PORTNAME= bowtie2
DISTVERSIONPREFIX= v
DISTVERSION= 2.5.0
DISTVERSION= 2.5.1
CATEGORIES= biology perl5 python
MAINTAINER= jwb@FreeBSD.org

6
biology/bowtie2/distinfo
View File

@ -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

28
biology/bowtie2/files/patch-Makefile
View File

@ -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