sci-biology/salmon: version bump 0.5/0.6, cleanup

Package-Manager: portage-2.2.20-prefix

8 files changed, 92 insertions, 17 deletions

diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
index df7ad78b6..91a74e7f4 100644
--- a/sci-biology/salmon/Manifest
+++ b/sci-biology/salmon/Manifest
@@ -1,2 +1,4 @@
 DIST salmon-0.3.2.tar.gz 1674131 SHA256 e0c957f0bc612e1fd7d7c4383758396042b68ea08aeae024cadb5d63e6dd9cf2 SHA512 d9db133d8fb009a4b23251bce209a869644eb6139e0e4b9133f947999e0be4c30039f5cb8617dc4b73977cd690837abb407549a619ef82e6bb82577ff082becf WHIRLPOOL e2f8f636547c93fbf3fade454754352537bc5a9fce668b0989ca58f5f5b9ca8f2454077af5dfc948f0acf9c6c2a6bdd6995d481dc08fd0f3db938639435afc0f
 DIST salmon-0.4.2.tar.gz 1711949 SHA256 702c4893a3c73a72bce68b2ff1283467f470df5c6be72c1b0fcb2470229d512b SHA512 28d823d3a97a46861972594d13737fe173583a0ac6dc2ebdc5f117e880493a057b34f8fea0d26fb2827d17ebcc38a06358dfea08db70f4a76c7fbe553f2b031d WHIRLPOOL bab133da989e10c19709c9a1ed8d8401b1e0e685fe5c2ebc75097b15b1670783c7747fd2137530426d892a2608c82d029bf82f94705a7a7052a425f179449700
+DIST salmon-0.5.0.tar.gz 1651002 SHA256 390f6535966117ead358af98b60d5c2f51e26d4d98e019df6778cfee9046c875 SHA512 c695cbbfbf6a8ecbb20a46bfcc428b3be458200b4296baa686b2ed4f664fa40a7db719620a8f2c1d1b482600d9d0f0cecfe5f00af6407e6fc6f8f263f227b4e0 WHIRLPOOL fdcc750bff9608c12c9462534222624c48dff1b7d8f029c77e2f83247ff85e1e7542793be09a1c501bfe0ac63a63c3f2cf854b3c1c90ee6abc76526382d61b2e
+DIST salmon-0.6.0.tar.gz 1639289 SHA256 2a015c0f95b745fbed575d8610aea7e09cb1af55ca2c68e10ab15826fba263b1 SHA512 74de1aee5629a975816977fd26fe6eca08fef90fe5f99ba652e7e08ea9b2ffcb5c144c270529db9ca8f982ae25219a56ca7f3844eef00d9c6c14f488a41f2f9b WHIRLPOOL 587b3d32e81a989cae50d4bb50982e36ae49d1ab2a017ce03fefd5972822b308c2e80832140c202f502f52e95ac5634bee7721828c6ddce4701426aeebe63e70
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 edc09e711..7ac3d0882 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 1d046766a..cb020ecde 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>mschu.dev@gmail.com</email>
-    <name>Michael Schubert</name>
-  </maintainer>
   <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">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 049344bbb..e64b220d3 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 dffe77e39..032fd4d52 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-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild
new file mode 100644
index 000000000..032fd4d52
--- /dev/null
+++ b/sci-biology/salmon/salmon-0.5.0.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="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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
+
+DEPEND="dev-libs/boost:0
+		dev-libs/jemalloc
+		dev-cpp/tbb"
+RDEPEND="${DEPEND}"
+
+src_install() {
+	cmake-utils_src_install
+	rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-0.6.0.ebuild b/sci-biology/salmon/salmon-0.6.0.ebuild
new file mode 100644
index 000000000..032fd4d52
--- /dev/null
+++ b/sci-biology/salmon/salmon-0.6.0.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="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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
+
+DEPEND="dev-libs/boost:0
+		dev-libs/jemalloc
+		dev-cpp/tbb"
+RDEPEND="${DEPEND}"
+
+src_install() {
+	cmake-utils_src_install
+	rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index ab171cb59..139e2ee9a 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
+}