[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/

[Christoph Junghans]

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