sci-biology/SPAdes: bump to 3.15.3

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

3 files changed, 40 insertions, 59 deletions

diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index e10186934..57f4fc569 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,4 +1,4 @@
-DIST SPAdes-3.15.1.tar.gz 13686155 BLAKE2B fb0ff0de93302268e1fc28199be3e14ef670aeab91fca82f2e895f899c9cd8d5380c31d4fe2e884737a917ff04a94cf55d25b91a27b47c91aa3e7c7408b9bd87 SHA512 b2ee4719937912f2b6326b67f602dc62f4be319ccf2774380a487da67fc2e32adcfa417ac5fcf4c5494f80152aab561b87e30a2d36abfe50ed1c48396b44d9d9
-DIST SPAdes-3.15.1_manual.html 78200 BLAKE2B b78da09ae94a46fbf4df19ba668276e6129083e7b50f66f86da137f8ed6435a2300b133be58fe25edb0cbb598aeb66e9310425574408bc419a3e3dff18893b15 SHA512 c3571abc87ffea1c54d7f0d42ce73955a7d101a4a61ecd104538832d193eab19c8813cf0a732f2bbe428724c24be283db89165900c2d49a7f3142770de4ca3b6
-DIST SPAdes-3.15.1_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
-DIST SPAdes-3.15.1_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
+DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4
+DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b
+DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
+DIST SPAdes-3.15.3_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
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
+}