commit: 1e1e01623ad2b04d0500d229995c50c3223dadcd
Author: mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Jan 23 21:38:55 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 28 10:25:28 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1e1e0162
sci-biology/salmon: version bump 0.5/0.6, cleanup
Package-Manager: portage-2.2.20-prefix
.../salmon/files/salmon-0.3.2-no-boost-static.patch | 4 ++--
sci-biology/salmon/metadata.xml | 8 ++++----
sci-biology/salmon/salmon-0.3.2.ebuild | 12 +++++++++---
sci-biology/salmon/salmon-0.4.2.ebuild | 12 +++++++++---
.../salmon/{salmon-0.4.2.ebuild => salmon-0.5.0.ebuild} | 12 +++++++++---
.../salmon/{salmon-0.4.2.ebuild => salmon-0.6.0.ebuild} | 12 +++++++++---
sci-biology/salmon/salmon-9999.ebuild | 15 ++++++++++-----
7 files changed, 52 insertions(+), 23 deletions(-)
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
index edc09e7..7ac3d08 100644
--- 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
@@ -2,8 +2,8 @@ Do not force static and multithreaded boost libs, use what is
available
Patch by Michael Schubert
---- CMakeLists.txt
-+++ CMakeLists.txt
+--- 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 )
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
index 1d04676..cb020ec 100644
--- a/sci-biology/salmon/metadata.xml
+++ b/sci-biology/salmon/metadata.xml
@@ -1,14 +1,14 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Michael Schubert</name>
- </maintainer>
<maintainer type="project">
<email>[email protected]</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <maintainer type="person">
+ <email>[email protected]</email>
+ <name>Michael Schubert</name>
+ </maintainer>
<upstream>
<remote-id type="github">COMBINE-lab/salmon</remote-id>
</upstream>
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild
b/sci-biology/salmon/salmon-0.3.2.ebuild
index 049344b..e64b220 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+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/salmon/salmon-0.4.2.ebuild
b/sci-biology/salmon/salmon-0.4.2.ebuild
index dffe77e..032fd4d 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.4.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+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/salmon/salmon-0.4.2.ebuild
b/sci-biology/salmon/salmon-0.5.0.ebuild
similarity index 73%
copy from sci-biology/salmon/salmon-0.4.2.ebuild
copy to sci-biology/salmon/salmon-0.5.0.ebuild
index dffe77e..032fd4d 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.5.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+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/salmon/salmon-0.4.2.ebuild
b/sci-biology/salmon/salmon-0.6.0.ebuild
similarity index 73%
copy from sci-biology/salmon/salmon-0.4.2.ebuild
copy to sci-biology/salmon/salmon-0.6.0.ebuild
index dffe77e..032fd4d 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+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/salmon/salmon-9999.ebuild
b/sci-biology/salmon/salmon-9999.ebuild
index ab171cb..139e2ee 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
-inherit git-r3 cmake-utils
+inherit cmake-utils git-r3
DESCRIPTION="Transcript-level quantification from RNA-seq reads using
lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon";
@@ -13,11 +13,16 @@ EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git";
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+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
+}
