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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     2e9f85acc8a4dfe99a06aeef66b0cc3eb4416799
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 16:21:46 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 16:21:46 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e9f85ac

sci-biology/sailfish: drop KEYWORDS, version bump

This package automatically downloads 3rd-party sources
instead of just compiling.

https://github.com/kingsfordgroup/sailfish/issues/80

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 .../{sailfish-0.9.2.ebuild => sailfish-0.10.0.ebuild} | 19 ++++++++++---------
 sci-biology/sailfish/sailfish-9999.ebuild             | 18 ++++++++++++++----
 2 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/sci-biology/sailfish/sailfish-0.9.2.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
similarity index 64%
rename from sci-biology/sailfish/sailfish-0.9.2.ebuild
rename to sci-biology/sailfish/sailfish-0.10.0.ebuild
index d4953a2a5..9d618076d 100644
--- a/sci-biology/sailfish/sailfish-0.9.2.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit cmake-utils
+inherit cmake-utils multilib
 
 DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
 HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
@@ -11,27 +11,28 @@ SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.t
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
 IUSE=""
 
 PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
 
 DEPEND="dev-libs/boost:0
 		dev-libs/jemalloc
-		dev-cpp/tbb"
+		dev-cpp/tbb
+		sci-biology/jellyfish:2"
 RDEPEND="${DEPEND}"
 # a C++-11 compliant compiler is needs, aka >=gcc-4.7
 
-# TODO: disable
-# [  7%] Performing download step (verify and extract) for 'libdivsufsort'
-#i
+# TODO: disable running wget/curl during src_compile
+# https://github.com/kingsfordgroup/sailfish/issues/80
 # contains bundled RapMap
-# contains bundled libdivsufsort-master
+# contains bundled libdivsufsort
 # contains bundled libgff
 # contains bundled jellyfish-2.2.3
-# contains bundled sparsehash-sparsehash-2.0.2
+# contains bundled sparsehash-2.0.2
 
 src_install() {
 	cmake-utils_src_install
 	rm -r "${ED}"/usr/tests || die
+	rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
 }

diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
index 6c37b858e..f31f16197 100644
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ b/sci-biology/sailfish/sailfish-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit cmake-utils git-r3
+inherit cmake-utils git-r3 multilib
 
 DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
 HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
@@ -14,14 +14,24 @@ LICENSE="GPL-3"
 SLOT="0"
 IUSE=""
 
-PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch )
+PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch )
 
 DEPEND="dev-libs/boost:0
 		dev-libs/jemalloc
-		dev-cpp/tbb"
+		dev-cpp/tbb
+		sci-biology/jellyfish:2"
 RDEPEND="${DEPEND}"
 
+# TODO: disable running wget/curl during src_compile
+# https://github.com/kingsfordgroup/sailfish/issues/80
+# contains bundled RapMap
+# contains bundled libdivsufsort-master
+# contains bundled libgff
+# contains bundled jellyfish-2.2.3
+# contains bundled sparsehash-2.0.2
+
 src_install() {
 	cmake-utils_src_install
 	rm -r "${ED}"/usr/tests || die
+	rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
 }