5 files changed, 102 insertions, 63 deletions
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index e10186934..cf724a82a 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-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd
+DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa
+DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
+DIST SPAdes-3.15.5_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-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
new file mode 100644
index 000000000..026dd0476
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+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-build/cmake"
+
+# Remove for next release:
+# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831
+PATCHES=(
+	"${FILESDIR}/${P}-gcc13.patch"
+)
+
+src_install(){
+	einstalldocs
+	# WORKAROUND: This script does both compile and install in one go
+	PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
new file mode 100644
index 000000000..3dd3f8c02
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch
@@ -0,0 +1,49 @@
+From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001
+From: Bo YU <tsu.yubo@gmail.com>
+Date: Wed, 19 Jul 2023 18:42:04 +0800
+Subject: [PATCH] fix build issues due to gcc-13
+
+Signed-off-by: Bo YU <tsu.yubo@gmail.com>
+---
+ ext/include/llvm/Support/Signals.h   | 1 +
+ src/common/pipeline/library_data.hpp | 1 +
+ src/common/sequence/nucl.hpp         | 2 ++
+ 3 files changed, 4 insertions(+)
+
+diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h
+index e0a18e72f..148216b8f 100644
+--- a/ext/include/llvm/Support/Signals.h
++++ b/ext/include/llvm/Support/Signals.h
+@@ -14,6 +14,7 @@
+ #ifndef LLVM_SUPPORT_SIGNALS_H
+ #define LLVM_SUPPORT_SIGNALS_H
+ 
++#include <cstdint>
+ #include <string>
+ 
+ namespace llvm {
+diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp
+index 3cbaf0adb..1ffaa7b37 100644
+--- a/src/common/pipeline/library_data.hpp
++++ b/src/common/pipeline/library_data.hpp
+@@ -8,6 +8,7 @@
+ 
+ #include <map>
+ #include <string>
++#include <cstdint>
+ 
+ // Forward decls for LLVM YAML API
+ namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } }
+diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp
+index 9c7d6de13..e10e7f583 100755
+--- a/src/common/sequence/nucl.hpp
++++ b/src/common/sequence/nucl.hpp
+@@ -8,6 +8,8 @@
+ #ifndef NUCL_HPP_
+ #define NUCL_HPP_
+ 
++#include <cstdint>
++
+ #include "utils/verify.hpp"
+ 
+ /**
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
index 0845ad7a4..5f573393e 100644
--- a/sci-biology/SPAdes/metadata.xml
+++ b/sci-biology/SPAdes/metadata.xml
@@ -10,8 +10,11 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<longdescription>
-truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
-hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
-dipspades is assembly module for highly polymorphic diploid genomes
-</longdescription>
+		truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
+		hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
+		dipspades is assembly module for highly polymorphic diploid genomes
+	</longdescription>
+	<upstream>
+		<remote-id type="github">ablab/spades</remote-id>
+	</upstream>
 </pkgmetadata>