diff options
Diffstat (limited to 'sci-biology/express')
-rw-r--r-- | sci-biology/express/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/express/express-0.9.5-r1.ebuild | 36 | ||||
-rw-r--r-- | sci-biology/express/express-0.9.5.ebuild | 35 | ||||
-rw-r--r-- | sci-biology/express/express-1.5.1.ebuild | 37 | ||||
-rw-r--r-- | sci-biology/express/files/express-1.5.1-buildsystem.patch | 55 | ||||
-rw-r--r-- | sci-biology/express/metadata.xml | 5 |
6 files changed, 170 insertions, 0 deletions
diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest new file mode 100644 index 000000000000..6edb1d9f6603 --- /dev/null +++ b/sci-biology/express/Manifest @@ -0,0 +1,2 @@ +DIST express-0.9.5-src.tgz 766024 SHA256 e17250d62750560c2dc9cb579f58784b5076afb74088f36523ddd623e08bc022 SHA512 3a7360ffbe57f4f712b6db38d551d31384d995050a86238d79299edb12f0e7f5dca6f362b7858b5051ea2879af2b3559f78f9780d75ef2ef6fdad7398f781403 WHIRLPOOL 290772dceca2465f922f5d5fe548dc8fd460422589697173c58f98dc3afa2e91175fe1fa52e5f29458ea6af74c8da609776fa583bf5efcb2d5771c4c9ad51cde +DIST express-1.5.1-src.tgz 931166 SHA256 0c5840a42da830fd8701dda8eef13f4792248bab4e56d665a0e2ca075aff2c0f SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee WHIRLPOOL 2c75385b2a2ec8f7b77df760344affc108e827eb9f59014f08af0cee0ca8806beeba101d13ed8b43883a25fc9486bd405f402339f0e4e394d3895694c75a4e2a diff --git a/sci-biology/express/express-0.9.5-r1.ebuild b/sci-biology/express/express-0.9.5-r1.ebuild new file mode 100644 index 000000000000..608ade0766ea --- /dev/null +++ b/sci-biology/express/express-0.9.5-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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/express-${PV}/express-${PV}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +CMAKE_USE_DIR="${S}/src" + +src_prepare() { + sed \ + -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \ + -e '1 a find_package(Boost 1.52 COMPONENTS filesystem program_options system thread)' \ + -e '1 a find_package(ZLIB)' \ + -e '/add_executable/ a include_directories("/usr/include/bamtools")' \ + -i src/CMakeLists.txt || die + + cmake-utils_src_prepare +} diff --git a/sci-biology/express/express-0.9.5.ebuild b/sci-biology/express/express-0.9.5.ebuild new file mode 100644 index 000000000000..a4fcff4be4f5 --- /dev/null +++ b/sci-biology/express/express-0.9.5.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-libs/boost + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +CMAKE_USE_DIR="${S}/src" + +src_prepare() { + sed \ + -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \ + -e '1 a find_package(Boost 1.46 COMPONENTS filesystem program_options thread)' \ + -e '1 a find_package(ZLIB)' \ + -e '/add_executable/ a include_directories("/usr/include/bamtools")' \ + -i src/CMakeLists.txt || die +} 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..231b1f878ba3 --- /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 +# $Id$ + +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}) diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/express/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> |