<pre style='margin:0'>
Marcus Calhoun-Lopez (MarcusCalhoun-Lopez) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/901c641d0185b175757c7a7e5b507bb9cbf39638">https://github.com/macports/macports-ports/commit/901c641d0185b175757c7a7e5b507bb9cbf39638</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 901c641d0185b175757c7a7e5b507bb9cbf39638
</span>Author: Marcus Calhoun-Lopez <mcalhoun@macports.org>
AuthorDate: Sat Jan 19 08:02:13 2019 -0700
<span style='display:block; white-space:pre;color:#404040;'> bowtie: update version 0.12.9->1.2.2_p1
</span>---
science/bowtie/Portfile | 28 ++++++-----
science/bowtie/files/patch-Makefile.diff | 79 ++++++++++++++++++++++++--------
2 files changed, 72 insertions(+), 35 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/Portfile b/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index dad65e3..e3ce63c 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,10 +1,11 @@
</span> # -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
PortSystem 1.0
<span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup github 1.0
</span>
name bowtie
<span style='display:block; white-space:pre;background:#ffe0e0;'>-version 0.12.9
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup BenLangmead bowtie 1.2.2_p1 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span> categories science biology
platforms darwin
maintainers nomaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -20,18 +21,19 @@ long_description Bowtie is ${description}. It aligns short DNA sequences \
</span> paired-end).
homepage http://bowtie-bio.sourceforge.net/
<span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites sourceforge:project/bowtie-bio/${name}/${version}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-use_zip yes
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-extract.suffix -src${extract.suffix}
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 e75b41d3cfa0ff69bf4cc19038613d15a8702c5d \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 61012d45dca1c782d8907f7f7ab1a45518687d4ea6d9baa8bebcde79e1053761 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 7701615
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 9f818e1e85abaf09ddc58cbe96f9cf735f0ca918 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 ed1581d6ed97271e6de2c1f826a3169f1d5495461cd6f31b2b8f02e5e4adeebf \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 7890653
</span>
patchfiles-append patch-Makefile.diff
<span style='display:block; white-space:pre;background:#e0ffe0;'>+supported_archs x86_64 ppc64
</span> installs_libs no
<span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:zlib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:tbb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> # replicate values from Makefile prior to patching
configure.optflags -O3
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -40,17 +42,13 @@ configure.pre_args
</span> configure.universal_args
configure.post_args {>> Makefile.macports.inc}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-destroot {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- xinstall -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie-build \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie-inspect \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ${destroot}${prefix}/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+destroot.args-append prefix=${prefix}
</span>
<span style='display:block; white-space:pre;background:#e0ffe0;'>+post-destroot {
</span> xinstall -d ${destroot}${prefix}/share/doc/${name}
xinstall -m 644 -W ${worksrcpath} \
AUTHORS \
<span style='display:block; white-space:pre;background:#ffe0e0;'>- COPYING \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LICENSE \
</span> MANUAL \
NEWS \
TUTORIAL \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/files/patch-Makefile.diff b/science/bowtie/files/patch-Makefile.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index 907e4a4..73d91e3 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/files/patch-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/files/patch-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,34 +1,73 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Respect MacPorts compiler & compiler flags.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- Makefile.orig 2012-12-14 20:15:42.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ Makefile 2019-01-19 07:27:34.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2,14 +2,16 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- Makefile.orig 2017-12-12 11:29:54.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile 2019-01-19 07:51:44.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2,16 +2,17 @@
</span> # Makefile for bowtie, bowtie-build, bowtie-inspect
#
<span style='display:block; white-space:pre;background:#e0ffe0;'>+-prefix = /usr/local
</span> +include Makefile.macports.inc
+
<span style='display:block; white-space:pre;background:#ffe0e0;'>- SEQAN_DIR = SeqAn-1.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- SEQAN_INC = -I $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- INC = $(SEQAN_INC)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- GCC_PREFIX = $(shell dirname `which gcc`)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- GCC_SUFFIX =
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++prefix ?= /usr/local
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bindir = $(prefix)/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SEQAN_DIR = ./SeqAn-1.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# treat SeqAn as a sysdir to suppress warnings
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SEQAN_INC = -isystem $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++SEQAN_INC = -I $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CPP = g++
</span> -CXX = $(CPP)
<span style='display:block; white-space:pre;background:#ffe0e0;'>-+CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+CXX ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CC = gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++CXX ?= g++
</span> +CPP ?= $(CXX)
<span style='display:block; white-space:pre;background:#e0ffe0;'>++CC ?= gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
</span> HEADERS = $(wildcard *.h)
<span style='display:block; white-space:pre;background:#ffe0e0;'>- BOWTIE_PTHREADS = 1
</span> BOWTIE_MM = 1
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -99,8 +101,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BITS_FLAG = -m64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -49,14 +50,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ MACOS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ifneq (,$(findstring Darwin,$(shell uname)))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ MACOS = 1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ifneq (,$(findstring 13,$(shell uname -r)))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- CPP = clang++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- CC = clang
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- override EXTRA_FLAGS += -stdlib=libstdc++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ifeq (1, $(RELEASE_BUILD))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- EXTRA_FLAGS += -mmacosx-version-min=10.9
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- endif
</span> endif
<span style='display:block; white-space:pre;background:#ffe0e0;'>--DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--RELEASE_FLAGS = -O3 $(BITS_FLAG)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+DEBUG_FLAGS = $(BITS_FLAG)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+RELEASE_FLAGS = $(BITS_FLAG)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LINUX =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -159,29 +152,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VERSION = $(shell cat VERSION)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-BITS=32
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ifeq (x86_64,$(shell uname -m))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- BITS=64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# msys will always be 32 bit so look at the cpu arch instead.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ifeq (1,$(MINGW))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- BITS=64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ifeq (1,$(LINUX))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ifeq (x86_64, $(shell uname -p))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- BITS=64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ifeq (32,$(BITS))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- $(error bowtie2 compilation requires a 64-bit platform )
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-DEBUG_FLAGS = -O0 -g3 -m64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-RELEASE_FLAGS = -O3 -m64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++DEBUG_FLAGS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++RELEASE_FLAGS =
</span> NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
</pre><pre style='margin:0'>
</pre>