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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-05-17 23:40:15 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-05-17 23:40:15 +0000 |
| commit | 1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef (patch) | |
| tree | 3e51699a34bf34d5fcbddbb7ef899e033c4012a0 /biology | |
| parent | 3d7c67ed7494413599dd96091054151f80f8d2a4 (diff) | |
| download | ports-1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef.tar.gz ports-1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef.zip | |
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*)
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bowtie2/Makefile | 11 | ||||
| -rw-r--r-- | biology/bowtie2/distinfo | 10 | ||||
| -rw-r--r-- | 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@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 |