commit: 01e354c4ff4b1404ab3fc884363af8b73a799c3c Author: layman <layman <AT> localhost> AuthorDate: Thu May 21 17:48:15 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Thu May 21 17:48:15 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=01e354c4
sci-biology/salmon: add salmon Package-Manager: portage-2.2.14-prefix sci-biology/salmon/ChangeLog | 11 ++++++++++ .../files/salmon-0.3.2-no-boost-static.patch | 16 +++++++++++++++ sci-biology/salmon/metadata.xml | 9 ++++++++ sci-biology/salmon/salmon-0.3.2.ebuild | 23 +++++++++++++++++++++ sci-biology/salmon/salmon-9999.ebuild | 24 ++++++++++++++++++++++ 5 files changed, 83 insertions(+) diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog new file mode 100644 index 0000000..83c1c81 --- /dev/null +++ b/sci-biology/salmon/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/salmon +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*salmon-0.3.2 (21 May 2015) +*salmon-9999 (21 May 2015) + + 21 May 2015; Michael Schubert <[email protected]> + +files/salmon-0.3.2-no-boost-static.patch, +metadata.xml, + +salmon-0.3.2.ebuild, +salmon-9999.ebuild: + sci-biology/salmon: add salmon diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch new file mode 100644 index 0000000..6a00ebe --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch @@ -0,0 +1,16 @@ +--- CMakeLists.txt.orig 2015-05-19 23:39:27.969165466 +0100 ++++ CMakeLists.txt 2015-05-19 23:39:40.154150194 +0100 +@@ -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/salmon/metadata.xml b/sci-biology/salmon/metadata.xml new file mode 100644 index 0000000..b7551a6 --- /dev/null +++ b/sci-biology/salmon/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Michael Schubert</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild new file mode 100644 index 0000000..59ab07e --- /dev/null +++ b/sci-biology/salmon/salmon-0.3.2.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" +HOMEPAGE="https://github.com/COMBINE-lab/salmon"; +SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch "${FILESDIR}/${P}-no-boost-static.patch" +} diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild new file mode 100644 index 0000000..e631316 --- /dev/null +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 cmake-utils + +DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" +HOMEPAGE="https://github.com/COMBINE-lab/salmon"; +SRC_URI="" +EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch "${FILESDIR}/${PN}-0.3.2-no-boost-static.patch" +}
