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

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

commit:     5bcbca87122d15ab6ae31547021b65c872cef1c5
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 17:17:12 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 17:17:12 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5bcbca87

sci-biology/salmon: document install procedure issues

The building procedure is still a mess.

https://github.com/COMBINE-lab/salmon/issues/19

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 .../{salmon-0.6.0.ebuild => salmon-0.9.1.ebuild}   |  4 +--
 sci-biology/salmon/salmon-9999.ebuild              | 29 +++++++++++++++++++---
 2 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/sci-biology/salmon/salmon-0.6.0.ebuild b/sci-biology/salmon/salmon-0.9.1.ebuild
similarity index 84%
rename from sci-biology/salmon/salmon-0.6.0.ebuild
rename to sci-biology/salmon/salmon-0.9.1.ebuild
index f88310f95..34a425403 100644
--- a/sci-biology/salmon/salmon-0.6.0.ebuild
+++ b/sci-biology/salmon/salmon-0.9.1.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=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
 DEPEND="dev-libs/boost:0
 		dev-libs/jemalloc
 		dev-cpp/tbb"

diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 4acc02e71..4f48644c6 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.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
@@ -14,12 +14,35 @@ LICENSE="GPL-3"
 SLOT="0"
 IUSE=""
 
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
 DEPEND="dev-libs/boost:0
 		dev-libs/jemalloc
 		dev-cpp/tbb"
 RDEPEND="${DEPEND}"
+# https://github.com/COMBINE-lab/salmon/issues/19
+#
+# contains bundled copies of https://github.com/jemalloc/jemalloc
+# https://github.com/gabime/spdlog
+# https://github.com/efficient/libcuckoo
+# https://github.com/greg7mdp/sparsepp
+# https://github.com/COMBINE-lab/RapMap
+# https://github.com/Kingsford-Group/libgff
+# sci-libs/io_lib
+#
+# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158
+# modified bwa copy
+#
+# and maybe more
+
+src_configure(){
+	local mycmakeargs=(
+		"-DBOOST_ROOT=${EPREFIX}/usr"
+		"-DTBB_INSTALL_DIR=${EPREFIX}/usr"
+		"-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr"
+	)
+	# BUG: the configure step run automatically curl download of 3rd-party stuff
+	# https://github.com/COMBINE-lab/salmon/issues/19
+	cmake-utils_src_configure
+}
 
 src_install() {
 	cmake-utils_src_install