[gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/, sci-biology/sailfish/files/

[Justin Lecher]

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-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <maintainer type="person">
+    <email>mschu.dev@×××××.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
+}