svn commit: r499544 - in head/biology/bowtie2: . files

[Jason W. Bacon]

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 at 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