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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2022-11-04 23:47:34 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2022-11-04 23:49:02 +0000 |
| commit | f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa (patch) | |
| tree | a1cb8541fda2d6ba4ec04f2ea88dbd8b96868427 | |
| parent | a6e687526d642989ff6fad1f4fd50ed15afa5abf (diff) | |
| download | ports-f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa.tar.gz ports-f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa.zip | |
biology/bowtie2: Update to 2.5.0
Performance improvements and minor improvements
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
| -rw-r--r-- | biology/bowtie2/Makefile | 2 | ||||
| -rw-r--r-- | biology/bowtie2/distinfo | 6 | ||||
| -rw-r--r-- | 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 |