sci-biology/express: Version BUmp; thanks Michael Schubert for the initial patch, #525188

Package-Manager: portage-2.2.14_rc1/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 120 insertions, 11 deletions

diff --git a/sci-biology/express/ChangeLog b/sci-biology/express/ChangeLog
index 6a0a592f12a0..51bc0c74b08c 100644
--- a/sci-biology/express/ChangeLog
+++ b/sci-biology/express/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/express
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/express/ChangeLog,v 1.5 2014/02/05 07:33:56 pinkbyte Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/express/ChangeLog,v 1.6 2014/10/13 07:56:29 jlec Exp $
+
+*express-1.5.1 (13 Oct 2014)
+
+  13 Oct 2014; Justin Lecher <jlec@gentoo.org> +express-1.5.1.ebuild,
+  +files/express-1.5.1-buildsystem.patch:
+  Version BUmp; thanks Michael Schubert for the initial patch, #525188
 
 *express-0.9.5-r1 (05 Feb 2014)
 
diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest
index 63e2d87e4840..5f3c7f30bc78 100644
--- a/sci-biology/express/Manifest
+++ b/sci-biology/express/Manifest
@@ -1,19 +1,30 @@
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 DIST express-0.9.5-src.tgz 766024 SHA256 e17250d62750560c2dc9cb579f58784b5076afb74088f36523ddd623e08bc022 SHA512 3a7360ffbe57f4f712b6db38d551d31384d995050a86238d79299edb12f0e7f5dca6f362b7858b5051ea2879af2b3559f78f9780d75ef2ef6fdad7398f781403 WHIRLPOOL 290772dceca2465f922f5d5fe548dc8fd460422589697173c58f98dc3afa2e91175fe1fa52e5f29458ea6af74c8da609776fa583bf5efcb2d5771c4c9ad51cde
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diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild
new file mode 100644
index 000000000000..9d9f50c6a49e
--- /dev/null
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/express/express-1.5.1.ebuild,v 1.1 2014/10/13 07:56:29 jlec Exp $
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="Streaming RNA-Seq Analysis"
+HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
+SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+	>=dev-libs/boost-1.52.0:=
+	dev-libs/protobuf
+	dev-util/google-perftools
+	sys-libs/zlib
+	sci-biology/bamtools"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-src"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-buildsystem.patch
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools"
+	)
+	cmake-utils_src_configure
+}
diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch
new file mode 100644
index 000000000000..fca5feadd111
--- /dev/null
+++ b/sci-biology/express/files/express-1.5.1-buildsystem.patch
@@ -0,0 +1,55 @@
+ CMakeLists.txt     | 8 +++-----
+ src/CMakeLists.txt | 4 ++--
+ 2 files changed, 5 insertions(+), 7 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index c768e28..65d5633 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
+ set(${PROJECT_NAME}_VERSION_MINOR 5)
+ set(${PROJECT_NAME}_VERSION_PATCH 1)
+ 
+-set(CMAKE_CXX_FLAGS "-Wall")
+-
+ set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")
+ set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}")
+ set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}")
+ 
+ set(CMAKE_BUILD_TYPE Release)
+-set(Boost_USE_STATIC_LIBS ON)
++set(Boost_USE_STATIC_LIBS OFF)
+ 
+ find_package(Boost 1.39
+     COMPONENTS
+@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
+ 
+ find_package(Protobuf)
+ if (PROTOBUF_FOUND)
+-  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
++  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE})
+ 	set(PROTO_INT 1)
+ else (PROTOBUF_FOUND)
+-  include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
++  include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE})
+ 	set(PROTO_INT 0)
+ endif(PROTOBUF_FOUND)
+ 
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 1cc0c01..8929d1f 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC)
+ if(WIN32)
+   set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib")
+ else(WIN32)
+-  set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread")
++  set(LIBRARIES ${LIBRARIES} "bamtools" "pthread")
+ endif(WIN32)
+ 
+ if (PROTOBUF_FOUND)
+-  set(LIBRARIES ${LIBRARIES} "libprotobuf.a")
++  set(LIBRARIES ${LIBRARIES} "protobuf")
+ endif(PROTOBUF_FOUND)
+ 
+ target_link_libraries(express ${LIBRARIES})