commit: a1d0487c37ba900c1f239f5d73f7d429f018359d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jun 24 14:01:12 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jun 24 14:01:12 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1d0487c
sci-biology/salmon: version bump, attempts to get boost picked up
cmake does not detect boost for me although the errors speak of pthread
and not boost. Older version could probably be dropped soon.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
.../salmon/{salmon-0.3.2.ebuild => salmon-0.10.2.ebuild} | 4 +---
sci-biology/salmon/salmon-0.3.2.ebuild | 2 +-
sci-biology/salmon/salmon-0.4.2.ebuild | 2 +-
sci-biology/salmon/salmon-0.5.0.ebuild | 2 +-
sci-biology/salmon/salmon-9999.ebuild | 10 +++++-----
5 files changed, 9 insertions(+), 11 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild
b/sci-biology/salmon/salmon-0.10.2.ebuild
similarity index 85%
copy from sci-biology/salmon/salmon-0.3.2.ebuild
copy to sci-biology/salmon/salmon-0.10.2.ebuild
index 6f5be90fb..34a425403 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -14,8 +14,6 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
-
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
dev-cpp/tbb"
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild
b/sci-biology/salmon/salmon-0.3.2.ebuild
index 6f5be90fb..b9a50ebd1 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild
b/sci-biology/salmon/salmon-0.4.2.ebuild
index f88310f95..42ccf1e6c 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.4.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/salmon/salmon-0.5.0.ebuild
b/sci-biology/salmon/salmon-0.5.0.ebuild
index f88310f95..42ccf1e6c 100644
--- a/sci-biology/salmon/salmon-0.5.0.ebuild
+++ b/sci-biology/salmon/salmon-0.5.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/salmon/salmon-9999.ebuild
b/sci-biology/salmon/salmon-9999.ebuild
index 4f48644c6..d370710b6 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -3,11 +3,10 @@
EAPI=6
-inherit cmake-utils git-r3
+inherit multilib cmake-utils git-r3
DESCRIPTION="Transcript-level quantification from RNA-seq reads using
lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon";
-SRC_URI=""
EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git";
LICENSE="GPL-3"
@@ -24,7 +23,7 @@ RDEPEND="${DEPEND}"
# https://github.com/gabime/spdlog
# https://github.com/efficient/libcuckoo
# https://github.com/greg7mdp/sparsepp
-# https://github.com/COMBINE-lab/RapMap
+# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it
# https://github.com/Kingsford-Group/libgff
# sci-libs/io_lib
#
@@ -35,11 +34,12 @@ RDEPEND="${DEPEND}"
src_configure(){
local mycmakeargs=(
- "-DBOOST_ROOT=${EPREFIX}/usr"
+ "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/"
+ "-DBOOST_LIBRARYDIR=${EPREFIX}/usr/$(get_libdir)/"
"-DTBB_INSTALL_DIR=${EPREFIX}/usr"
"-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr"
)
- # BUG: the configure step run automatically curl download of 3rd-party
stuff
+ # BUG: the configure step runs automatically curl download of 3rd-party
stuff
# https://github.com/COMBINE-lab/salmon/issues/19
cmake-utils_src_configure
}
