sci-biology/SPAdes: version bump

- BiosyntheticSPAdes pipeline for identifying Biosynthetic Gene Clusters (BGCs)
- Hybrid transcriptome assembly (Illumina RNA-Seq + Iso-seq / ONT RNA)
- Plasmid assembly from metagenomic datasets
- New --isolate option that improves assembly quality of standard datasets with
  high coverage
- New standalone tools for read filtration based on k-mer coverage and
  estimating number of unique k-mers in reads
- Improved SPAligner tool for read-to-graph alignment
- Major performance improvements and memory consumption reduction in graph
  construction, simplification procedures and throughout the whole pipeline
- Several bug-fixes.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

3 files changed, 80 insertions, 1 deletions

diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index fba8980d4..87f33dd2f 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -3,3 +3,8 @@ DIST SPAdes-3.13.0_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d7
 DIST SPAdes-3.13.0_manual.html 64051 BLAKE2B 6217855724637fd7615d194747fcec6a94f259e3534c52574183d8bcb9cc2bf75435989f75e77774b19d6268aa6eeeb525db8ee305d02419480e285637db971a SHA512 4c80ec091ca3478e26c911313465a886c7768f87574b69a651e7e1519eef73e2bdf147e2d4136993fd309802c0fc9380ffff9a05f2da3aec5db69bbf7cd3af75
 DIST SPAdes-3.13.0_rnaspades_manual.html 7109 BLAKE2B c560e781b97899b02abf1324506a505fafa8819dd2dcf33a60886b19ddb4af515901d3ee4ac98a0d9aa21939e1afa040b0063b287f46b9b02202d5a562ba28b4 SHA512 26761374a6baa706139c108e2695ec56aef8aa1433c72e20b8b73a5e8204a225a9b1e79fddb4f627196005c7e843be8df4a7cd02a653cc47f3a9f8934d96160f
 DIST SPAdes-3.13.0_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b
+DIST SPAdes-3.14.0.tar.gz 12169054 BLAKE2B ae09a9d73985e91d10006a237768f896ddabbb01dfca4cab7095683f9948579fd8e94f3d5dbc7cccf7e90c5d6ddabb05b7dfeee8409cba0f2143511d82f6a1a0 SHA512 ad862275805559193369a7d04687fe0503a3a956f67f0d822950af634c2508773457eb0efc980b1faf7bf28768858d6495a0b485945168f4be4193ad7de2809a
+DIST SPAdes-3.14.0_dipspades_manual.html 12561 BLAKE2B adacd4a195a1ae4ce400907d728aa9df9398ffd8545777dc2d5a69cab4396e73825e4e8f42d3d590cf82ec4f6cbb0e4783d3d731b6637b0ce8cf8afe2ebe689b SHA512 618284c899b5c0f167b91638ac3ca4d7ee2c932f5acbfa6225f43276b073259000022f12afa3d8df26dfd967085b3d2d11ca006766169199afc02de111a78db4
+DIST SPAdes-3.14.0_manual.html 71118 BLAKE2B 909a9a1d5a16a1bfa899eab630f48984f92554778caf2f32402d9187a51ff8247fad03facc5f94638cabe3e56cfaea502912c80214352c82b660b167ffe2231f SHA512 c224bc17e3aee540454ea8afe03cd3f9c47c7e9e3f5f52ae03dc5f00ce0bae48e9f4ebba985a3c7f0429145850c36cc2ac931550fba0389cc18a87924c874655
+DIST SPAdes-3.14.0_rnaspades_manual.html 7467 BLAKE2B d69ccf162978a68c2e85a473b79d87c4a3ffc7a35791f4e57e6885a28fd15a359dca2b229d174e9ab835c69a2417db2d8b94b82c5f33e51bb6e19dbbfd79d794 SHA512 ba099f3902edd3d10bb0556eab5cdd571ae1a39689f2abee24bf342f1a30189df46baa5d1d6793d66191a4fb15ed58d8753c6b9b4aa09b051332323c621d9952
+DIST SPAdes-3.14.0_truspades_manual.html 10769 BLAKE2B ec2788a9dfdb783b8e922517263d54177595c4c6b6feee7d4c6122c3c7db561a8e2f31d210af1d6384aeb9554fb551a3ddb9937bcaf185ad6707d8c3f049f48a SHA512 e19a9385ae63f32cb232c90abd16eb8563b6b8f0abcdb2aadcfdf35cfe4aee8cf329fc97e5a2a7149ac9c6fce40791b5a89c9431de90d6e1d3651b6f0a5e221b
diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
index 00ccc4f27..d3c1e0a57 100644
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
diff --git a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild b/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
new file mode 100644
index 000000000..d3c1e0a57
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_{4,5}} )
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="http://cab.spbu.ru/software/spades"
+SRC_URI="
+	https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+	http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+	http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+	http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html
+	http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html -> ${P}_dipspades_manual.html"
+# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid genomes
+#	(still present in the release but no longer supported)
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-python/regex"
+RDEPEND="${DEPEND}"
+# 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
+
+pkg_pretend() {
+	if [[ ${MERGE_TYPE} != binary ]]; then
+		if [[ $(tc-getCXX) == *g++ ]] ; then
+			if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then
+				eerror "You need at least sys-devel/gcc-4.7.0"
+				die "You need at least sys-devel/gcc-4.7.0"
+			fi
+		fi
+	fi
+}
+
+src_compile(){
+	PREFIX="${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
+}