Date: Sun, 21 Apr 2019 15:23:26 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r499544 - in head/biology/bowtie2: . files Message-ID: <201904211523.x3LFNQnk092905@repo.freebsd.org>
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Author: jwb Date: Sun Apr 21 15:23:25 2019 New Revision: 499544 URL: https://svnweb.freebsd.org/changeset/ports/499544 Log: biology/bowtie2: Upgrade to 2.3.5.1 Disable aarch64. Upstream support has changed and I lack the resources to develop new patches. Modified: head/biology/bowtie2/Makefile head/biology/bowtie2/distinfo head/biology/bowtie2/files/patch-Makefile head/biology/bowtie2/pkg-plist Modified: head/biology/bowtie2/Makefile ============================================================================== --- head/biology/bowtie2/Makefile Sun Apr 21 14:44:23 2019 (r499543) +++ head/biology/bowtie2/Makefile Sun Apr 21 15:23:25 2019 (r499544) @@ -2,7 +2,7 @@ PORTNAME= bowtie2 DISTVERSIONPREFIX= v -DISTVERSION= 2.3.5 +DISTVERSION= 2.3.5.1 CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org @@ -12,16 +12,16 @@ LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE # May also work on other 64-bit platforms, but untested -ONLY_FOR_ARCHS= aarch64 amd64 -BROKEN_aarch64= usage: dirname string [...] - +ONLY_FOR_ARCHS= amd64 LIB_DEPENDS= libtbb.so:devel/tbb +RUN_DEPENDS= bash:shells/bash USES= gmake localbase:ldflags perl5 python shebangfix USE_PERL5= run USE_GITHUB= yes -SHEBANG_FILES= bowtie2 bowtie2-build bowtie2-inspect scripts/*.pl +SHEBANG_FILES= bowtie2 bowtie2-build bowtie2-inspect \ + scripts/bowtie2-hbb.sh scripts/*.pl GH_ACCOUNT= BenLangmead OPTIONS_DEFINE= DOCS EXAMPLES Modified: head/biology/bowtie2/distinfo ============================================================================== --- head/biology/bowtie2/distinfo Sun Apr 21 14:44:23 2019 (r499543) +++ head/biology/bowtie2/distinfo Sun Apr 21 15:23:25 2019 (r499544) @@ -1,3 +1,3 @@ -TIMESTAMP = 1552832567 -SHA256 (BenLangmead-bowtie2-v2.3.5_GH0.tar.gz) = c5daeb0249e98dfe8f70dac7d660b100365a00a22df4cad94d3e383f489911ae -SIZE (BenLangmead-bowtie2-v2.3.5_GH0.tar.gz) = 10584383 +TIMESTAMP = 1555781941 +SHA256 (BenLangmead-bowtie2-v2.3.5.1_GH0.tar.gz) = 86a018af1090900c160a0990cc106569805aa64a3ec8708e1d2127839e4a94b4 +SIZE (BenLangmead-bowtie2-v2.3.5.1_GH0.tar.gz) = 10587039 Modified: head/biology/bowtie2/files/patch-Makefile ============================================================================== --- head/biology/bowtie2/files/patch-Makefile Sun Apr 21 14:44:23 2019 (r499543) +++ head/biology/bowtie2/files/patch-Makefile Sun Apr 21 15:23:25 2019 (r499544) @@ -1,4 +1,4 @@ ---- Makefile.orig 2019-03-16 04:14:43 UTC +--- Makefile.orig 2019-04-17 02:40:25 UTC +++ Makefile @@ -21,8 +21,9 @@ # Makefile for bowtie, bowtie2-build, bowtie2-inspect @@ -7,18 +7,46 @@ -prefix := /usr/local -bindir := $(prefix)/bin +# Use PREFIX (upper case) provided by many package managers -+PREXIX ?= /usr/local ++PREFIX ?= /usr/local +bindir := $(PREFIX)/bin LDLIBS := -lz GCC_PREFIX := $(shell dirname `which gcc`) -@@ -30,7 +31,8 @@ GCC_SUFFIX := +@@ -30,8 +31,9 @@ GCC_SUFFIX := CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) CXX ?= $(CPP) -CXXFLAGS += -std=c++98 +-ifeq (aarch64,$(shell uname -m)) +# long long is unsupported in c++98 +# CXXFLAGS += -std=c++98 - ifeq (aarch64,$(shell uname -m)) - CXXFLAGS += -fopenmp-simd -DWITH_AARCH64 ++ifeq (aarch64,$(shell uname -p)) + CXXFLAGS += -fopenmp-simd CPPFLAGS += -Ithird_party/simde + endif +@@ -198,13 +200,13 @@ SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c) + VERSION := $(shell cat VERSION) + + BITS := 32 +-ifeq (x86_64,$(shell uname -m)) ++ifeq (x86_64,$(shell uname -p)) + BITS := 64 + endif +-ifeq (amd64,$(shell uname -m)) ++ifeq (amd64,$(shell uname -p)) + BITS := 64 + endif +-ifeq (aarch64,$(shell uname -m)) ++ifeq (aarch64,$(shell uname -p)) + BITS := 64 + endif + # msys will always be 32 bit so look at the cpu arch instead. +@@ -219,7 +221,7 @@ endif + + SSE_FLAG := -msse2 + M64_FLAG := -m64 +-ifeq (aarch64,$(shell uname -m)) ++ifeq (aarch64,$(shell uname -p)) + SSE_FLAG = + M64_FLAG = + endif Modified: head/biology/bowtie2/pkg-plist ============================================================================== --- head/biology/bowtie2/pkg-plist Sun Apr 21 14:44:23 2019 (r499543) +++ head/biology/bowtie2/pkg-plist Sun Apr 21 15:23:25 2019 (r499544) @@ -8,6 +8,7 @@ bin/bowtie2-inspect bin/bowtie2-inspect-l bin/bowtie2-inspect-s bin/bowtie2-test +%%DATADIR%%/scripts/bowtie2-hbb.sh %%DATADIR%%/scripts/convert_quals.pl %%DATADIR%%/scripts/gen_2b_occ_lookup.pl %%DATADIR%%/scripts/gen_occ_lookup.pl
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