commit: 59c62dccda24a226ceb535dee59e081c4f1002eb
Author: Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Thu Feb 5 21:54:51 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb 6 20:24:01 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=59c62dcc
Updated sci-biology/bowtie. Bowtie1 is now properly slotted in SLOT=1.
Additional build system fixes.
---
sci-biology/bowtie/bowtie-1.1.1.ebuild | 42 ++++++++++++++++++++++
.../{bowtie-2.1.0.ebuild => bowtie-2.2.4.ebuild} | 14 ++++----
.../bowtie/files/bowtie-1.1.1-buildsystem.patch | 37 +++++++++++++++++++
...system.patch => bowtie-2.2.4-buildsystem.patch} | 21 ++++++-----
4 files changed, 97 insertions(+), 17 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild
b/sci-biology/bowtie/bowtie-1.1.1.ebuild
new file mode 100644
index 0000000..ad20591
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit base eutils toolchain-funcs
+
+DESCRIPTION="An ultrafast memory-efficient short read aligner"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/";
+SRC_URI="mirror://sourceforge/bowtie-bio/bowtie-1.1.1-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~x64-macos"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+
+src_compile() {
+ unset CFLAGS
+ emake \
+ CXX="$(tc-getCXX)" \
+ EXTRA_FLAGS="${LDFLAGS}" \
+ RELEASE_FLAGS="${CXXFLAGS}"
+}
+
+src_install() {
+ dobin bowtie bowtie-*
+ exeinto /usr/share/${PN}/scripts
+ doexe scripts/*
+
+ insinto /usr/share/${PN}
+ doins -r genomes indexes
+
+ newman MANUAL bowtie.1
+ dodoc AUTHORS NEWS TUTORIAL doc/README
+ dohtml doc/{manual.html,style.css}
+}
diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild
b/sci-biology/bowtie/bowtie-2.2.4.ebuild
similarity index 82%
rename from sci-biology/bowtie/bowtie-2.1.0.ebuild
rename to sci-biology/bowtie/bowtie-2.2.4.ebuild
index aedf017..19e0bca 100644
--- a/sci-biology/bowtie/bowtie-2.1.0.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.4.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
-inherit eutils toolchain-funcs
+inherit base eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/";
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/";
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
LICENSE="GPL-3"
@@ -21,6 +21,8 @@ DEPEND="${RDEPEND}
S="${WORKDIR}/${PN}2-${PV}"
+PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
+
pkg_pretend() {
grep "sse2" /proc/cpuinfo > /dev/null
if [[ $? -ne 0 ]] ; then
@@ -28,14 +30,10 @@ pkg_pretend() {
fi
}
-src_prepare() {
- epatch "${FILESDIR}/${P}-buildsystem.patch"
-}
-
src_compile() {
emake \
CC="$(tc-getCC)" \
- CPP="$(tc-getCXX)" \
+ CXX="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2"
}
diff --git a/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
new file mode 100644
index 0000000..9563a33
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-1.1.1-buildsystem.patch
@@ -0,0 +1,37 @@
+--- Makefile
++++ Makefile
+@@ -5,16 +5,11 @@
+ SEQAN_DIR = SeqAn-1.1
+ SEQAN_INC = -I $(SEQAN_DIR)
+ INC = $(SEQAN_INC) -I third_party
+-CPP = g++
+-CXX = $(CPP)
+-CC = gcc
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 1
+ EXTRA_FLAGS =
+-EXTRA_CFLAGS =
+ EXTRA_CXXFLAGS =
+-CFLAGS += $(EXTRA_CFLAGS)
+ CXXFLAGS += $(EXTRA_CXXFLAGS)
+
+ # Detect Cygwin or MinGW
+@@ -127,7 +122,7 @@
+ endif
+
+ DEBUG_FLAGS = -O0 -g3 -m64
+-RELEASE_FLAGS = -O3 -m64
++RELEASE_FLAGS = $(CXXFLAGS)
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+
+@@ -198,7 +193,7 @@
+ $(MM_DEF) \
+ $(SHMEM_DEF)
+
+-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
++ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS)
+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
+ RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
+
diff --git a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
similarity index 55%
rename from sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
rename to sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
index 97300b1..8b9218b 100644
--- a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
+++ b/sci-biology/bowtie/files/bowtie-2.2.4-buildsystem.patch
@@ -1,19 +1,22 @@
---- Makefile.old 2013-09-22 12:07:12.606844000 +0200
-+++ Makefile 2013-09-22 13:06:03.113888200 +0200
-@@ -24,8 +24,6 @@
+--- Makefile
++++ Makefile
+@@ -22,11 +22,6 @@
+ #
+
INC =
- GCC_PREFIX = $(shell dirname `which gcc`)
- GCC_SUFFIX =
+-GCC_PREFIX = $(shell dirname `which gcc`)
+-GCC_SUFFIX =
-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
- CXX = $(CPP)
+-CXX = $(CPP)
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
-@@ -141,7 +139,7 @@
+ BOWTIE_SHARED_MEM = 0
+@@ -152,7 +147,7 @@
- DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG)
DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
--RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
+-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
+RELEASE_FLAGS = $(CXXFLAGS)
RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
