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biology/bowtie2: Update to 2.4.3

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Drop tbb dependency (upstream switched to C++ threads)
Add support for powerpc64

Reported by:    portscout
Tested by:      pkubaj (powerpc64*)
This commit is contained in:
Jason W. Bacon 2021-05-17 18:40:15 -05:00
parent 3d7c67ed74
commit 1effaacbaf
3 changed files with 26 additions and 43 deletions
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11
biology/bowtie2/Makefile
View File

@ -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

10
biology/bowtie2/distinfo
View File

@ -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

48
biology/bowtie2/files/patch-Makefile
View File

@ -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,$(shell uname -p))
-ifneq (,$(findstring $(shell uname -m), x86_64 amd64))
+ifneq (,$(findstring $(shell uname -p), x86_64 amd64))
BITS := 64
-else ifeq (amd64,$(shell uname -m))
+else ifeq (amd64,$(shell uname -p))
BITS := 64
-else ifeq (aarch64,$(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