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

["Andrew Ammerlaan" <andrewammerlaan@riseup.net>]

commit:     89b29b2a57824d3a32051c4f8aa2eae6eb21bfab
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 15:28:59 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 15:28:59 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=89b29b2a

sci-biology/salmon: add version 1.4.0

Closes: https://github.com/gentoo/sci/pull/1013
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/salmon/salmon-1.4.0.ebuild | 40 +++++++++++++++++
 sci-biology/salmon/salmon-9999.ebuild  | 81 ++++++++++------------------------
 2 files changed, 63 insertions(+), 58 deletions(-)

diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
new file mode 100644
index 000000000..858ff642b
--- /dev/null
+++ b/sci-biology/salmon/salmon-1.4.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+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 -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+
+RDEPEND="
+	dev-libs/boost:=[threads]
+	sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+	app-arch/bzip2
+	app-arch/xz-utils
+	>=dev-libs/jemalloc-5.0.1
+	>=dev-cpp/tbb-2018.20180312
+	sci-biology/pufferfish
+	sci-libs/staden-io
+	sci-libs/libgff
+	dev-libs/cereal
+"
+
+BDEPEND="
+	app-arch/unzip
+	net-misc/curl
+"
+
+PATCHES=(
+	"${FILESDIR}/${P}-do-not-fetch-pufferfish.patch"
+	"${FILESDIR}/${P}-allow-newer-boost.patch"
+)

diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 8862ff790..b7d02edd7 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -1,69 +1,34 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit multilib cmake-utils git-r3
+inherit cmake git-r3
 
 DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
 HOMEPAGE="https://github.com/COMBINE-lab/salmon"
 EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
-#SRC_URI="https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
-#    https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
-#    https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
-#    https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
-#    https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
-#    https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 
-PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch
-	"${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
-	"${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
-	"${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
-	"${FILESDIR}"/salmon-0.10.2_fix_tests.patch
-	"${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-#    actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-#    https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-DEPEND="net-misc/curl
-		app-arch/unzip
-		sys-libs/zlib
-		app-arch/bzip2
-		app-arch/xz-utils
-		dev-libs/boost:0[threads]
-		>=dev-libs/jemalloc-5.0.1
-		>=dev-cpp/tbb-2018.20180312"
-RDEPEND="${DEPEND}"
-
-# https://github.com/COMBINE-lab/salmon/issues/19
-#
-# contains bundled copies of https://github.com/jemalloc/jemalloc
-# https://github.com/gabime/spdlog
-# https://github.com/efficient/libcuckoo
-# https://github.com/greg7mdp/sparsepp
-# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it
-# https://github.com/Kingsford-Group/libgff
-# sci-libs/io_lib
-#
-# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158
-# modified bwa copy
-#
-# and maybe more
-
-# See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
+RDEPEND="
+	dev-libs/boost:=[threads]
+	sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+	app-arch/bzip2
+	app-arch/xz-utils
+	>=dev-libs/jemalloc-5.0.1
+	>=dev-cpp/tbb-2018.20180312
+	sci-biology/pufferfish
+	sci-libs/staden-io
+	sci-libs/libgff
+	dev-libs/cereal
+"
+
+BDEPEND="
+	app-arch/unzip
+	net-misc/curl
+"