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

["Andrew Ammerlaan" <andrewammerlaan@gentoo.org>]

commit:     34773140d758b76b35f70f857f7b27ee06503921
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 14:24:18 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 14:24:18 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=34773140

sci-biology/SPAdes: bump to 3.15.3

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/SPAdes/SPAdes-3.15.1.ebuild | 55 ---------------------------------
 sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 36 +++++++++++++++++++++
 2 files changed, 36 insertions(+), 55 deletions(-)

diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
deleted file mode 100644
index 853524984..000000000
--- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="https://cab.spbu.ru/software/spades"
-SRC_URI="
-	https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
-	https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
-	https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
-	https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
-	sys-libs/zlib
-	app-arch/bzip2
-	dev-python/regex"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-util/cmake"
-# BUG:
-# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used,
-# not *.so or *.a are even used)
-#
-# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
-#      existing packages
-# nlopt
-# llvm
-# python_libs
-# bamtools
-# ConsensusCore
-# ssw
-# jemalloc
-# htrie
-# getopt_pp
-# cppformat
-# cityhash
-# samtools
-# bwa
-
-# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary?
-# bwa-0.7.12
-# bwa-0.6.2
-
-src_compile(){
-	PREFIX="${ED}"/usr ./spades_compile.sh || die
-}
-
-src_install(){
-	# BUG: move *.py files to standard site-packages/ subdirectories
-	insinto /usr/share/"${PN}"
-	dodoc "${DISTDIR}"/${P}_*manual.html
-}

diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
new file mode 100644
index 000000000..553c21e21
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="https://cab.spbu.ru/software/spades"
+SRC_URI="
+	https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+	https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+	https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+	https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-python/regex
+	${PYTHON_DEPS}
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-util/cmake"
+
+src_install(){
+	einstalldocs
+	# WORKAROUND: This script does both compile and install in one go
+	PREFIX="${ED}"/usr ./spades_compile.sh || die
+}