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author | mschubert <mschu.dev@gmail.com> | 2016-01-23 21:59:18 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2016-02-28 10:43:14 +0000 |
commit | 78cab883d2457b52fb12f8a72ec7ce29c0d51950 (patch) | |
tree | 066b658cdaa9b264a5102d73bf801787f00bde9c | |
parent | sci-biology/salmon: bump EAPI=6 (diff) | |
download | sci-78cab883d2457b52fb12f8a72ec7ce29c0d51950.tar.gz sci-78cab883d2457b52fb12f8a72ec7ce29c0d51950.tar.bz2 sci-78cab883d2457b52fb12f8a72ec7ce29c0d51950.zip |
sci-biology/sailfish: add ebuild
Package-Manager: portage-2.2.20-prefix
-rw-r--r-- | sci-biology/sailfish/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch | 20 | ||||
-rw-r--r-- | sci-biology/sailfish/metadata.xml | 15 | ||||
-rw-r--r-- | sci-biology/sailfish/sailfish-0.9.1.ebuild | 28 | ||||
-rw-r--r-- | sci-biology/sailfish/sailfish-9999.ebuild | 28 |
5 files changed, 92 insertions, 0 deletions
diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest new file mode 100644 index 000000000..022dbb249 --- /dev/null +++ b/sci-biology/sailfish/Manifest @@ -0,0 +1 @@ +DIST sailfish-0.9.1.tar.gz 1616817 SHA256 c3e74bb95501618ba34883395ac84f07504e038200936b5c03cab269ab60f1de SHA512 3765ddb7ba64d34757cb71e0a7255759f7c6e53ee1d45ac744ed12f98f9025e9a05d9b49a681c6e90b265d2e08b6591444b575d0933b2737d01f417602f5010e WHIRLPOOL 7614e9d6bb72718ee63648ef698484b378d0945f2da44dc560f0a5f5bea5336dfe358fbd801e9254cbc2d4fdf0bbd3a4ea82adae4e90e3cdcda26d93295a381d 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 000000000..7ac3d0882 --- /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 000000000..2831ceb14 --- /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-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="person"> + <email>mschu.dev@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 000000000..c17ea2988 --- /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 000000000..2d60e34cb --- /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 +} |