commit: 78cab883d2457b52fb12f8a72ec7ce29c0d51950 Author: mschubert <mschu.dev <AT> gmail <DOT> com> AuthorDate: Sat Jan 23 21:59:18 2016 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Feb 28 10:43:14 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=78cab883
sci-biology/sailfish: add ebuild Package-Manager: portage-2.2.20-prefix .../files/sailfish-0.9.1-no-boost-static.patch | 20 ++++++++++++++++ sci-biology/sailfish/metadata.xml | 15 ++++++++++++ sci-biology/sailfish/sailfish-0.9.1.ebuild | 28 ++++++++++++++++++++++ sci-biology/sailfish/sailfish-9999.ebuild | 28 ++++++++++++++++++++++ 4 files changed, 91 insertions(+) diff --git a/sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch new file mode 100644 index 0000000..7ac3d08 --- /dev/null +++ b/sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch @@ -0,0 +1,20 @@ +Do not force static and multithreaded boost libs, use what is available + +Patch by Michael Schubert + +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH ) + set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) + endif ( DEFINED CUSTOM_BOOST_PATH ) + +-## +-# We want static, multithreaded boost libraries +-## +-set (Boost_USE_STATIC_LIBS ON) +-set (Boost_USE_MULTITHREADED ON) +-#set (Boost_USE_STATIC_RUNTIME OFF) +- + find_package (ZLIB) + if (NOT ZLIB_FOUND) + message (FATAL_ERROR "zlib must be installed before configuration & building can proceed") diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml new file mode 100644 index 0000000..2831ceb --- /dev/null +++ b/sci-biology/sailfish/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="person"> + <email>mschu....@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">kingsfordgroup/sailfish</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/sailfish/sailfish-0.9.1.ebuild b/sci-biology/sailfish/sailfish-0.9.1.ebuild new file mode 100644 index 0000000..c17ea29 --- /dev/null +++ b/sci-biology/sailfish/sailfish-0.9.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" +HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/" +SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch ) + +DEPEND="dev-libs/boost:0 + dev-libs/jemalloc + dev-cpp/tbb" +RDEPEND="${DEPEND}" + +src_install() { + cmake-utils_src_install + rm -r "${ED}"/usr/tests || die +} diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild new file mode 100644 index 0000000..2d60e34 --- /dev/null +++ b/sci-biology/sailfish/sailfish-9999.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils git-r3 + +DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" +HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch ) + +DEPEND="dev-libs/boost:0 + dev-libs/jemalloc + dev-cpp/tbb" +RDEPEND="${DEPEND}" + +src_install() { + cmake-utils_src_install + rm -r "${ED}"/usr/tests || die +}