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

6 files changed, 34 insertions, 8 deletions

diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
index f31b52875..06187fd6c 100644
--- a/sci-biology/salmon/Manifest
+++ b/sci-biology/salmon/Manifest
@@ -1,3 +1,4 @@
+DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
 DIST salmon-0.3.2.tar.gz 1674131 BLAKE2B 2b6d124a01900db3e9a4c6c97b3559f0240a8376b612455bedce9187e5e73cb241ffe22128ba0af48c9f93d8f7862cce2d0692db6c76692e8556aae94e05b5c1 SHA512 d9db133d8fb009a4b23251bce209a869644eb6139e0e4b9133f947999e0be4c30039f5cb8617dc4b73977cd690837abb407549a619ef82e6bb82577ff082becf
 DIST salmon-0.4.2.tar.gz 1711949 BLAKE2B 0f4be6b394a0c37a3d721e89cfc5e3b28872128074fd805f2680b9a2d14e7cffc9416b3cff5b04867f84778f23d7a26bff6a1d09e2200c18c036367b24938759 SHA512 28d823d3a97a46861972594d13737fe173583a0ac6dc2ebdc5f117e880493a057b34f8fea0d26fb2827d17ebcc38a06358dfea08db70f4a76c7fbe553f2b031d
 DIST salmon-0.5.0.tar.gz 1651002 BLAKE2B dbeaa2ea5c63cd5a82a487224c215d92ce701ba45e73e6b71e51f22f0638b7dc9744f7bf5d4574ed670e99b79944bc1026df71036f7626e383308ede631ab214 SHA512 c695cbbfbf6a8ecbb20a46bfcc428b3be458200b4296baa686b2ed4f664fa40a7db719620a8f2c1d1b482600d9d0f0cecfe5f00af6407e6fc6f8f263f227b4e0
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
new file mode 100644
index 000000000..34a425403
--- /dev/null
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-libs/boost:0
+		dev-libs/jemalloc
+		dev-cpp/tbb"
+RDEPEND="${DEPEND}"
+
+src_install() {
+	cmake-utils_src_install
+	rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-0.3.2.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
 }