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

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

[Martin Mokrejs]

commit:     a5760c4470004861915035e9baf62ae5da7e8454
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 13 21:47:11 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 13 21:47:11 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a5760c44

sci-biology/SPAdes: fix compile issue but drop KEYWORDS because of QA issues

Use patch from https://github.com/Homebrew/homebrew-science/pull/5616
The package install its own *.py files outside of PYTHON's site-packages/.
The "make install" procedure is flakey shellscript and there is no setup.py so we could
reuse common infrastructure for pythonic packages.
There are plenty of bundled 3rd-party apps, some of them compiling statically.

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/SPAdes/SPAdes-3.10.1.ebuild            | 47 +++++++++++++++++-----
 .../files/SPAdes-3.10.1-fix-missing-include.patch  | 10 +++++
 2 files changed, 48 insertions(+), 9 deletions(-)

diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index 36f724d83..73050c1e4 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -12,13 +12,13 @@ HOMEPAGE="http://bioinf.spbau.ru/en/spades"
 SRC_URI="
 	http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
 	http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html
-	http://spades.bioinf.spbau.ru/release3.9.1/dipspades_manual.html -> ${P}_dipspades_manual.html
-	http://spades.bioinf.spbau.ru/release3.9.1/rnaspades_manual.html -> ${P}_rnaspades_manual.html
-	http://spades.bioinf.spbau.ru/release3.9.1/truspades_manual.html -> ${P}_truspades_manual.html"
+	http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html -> ${P}_dipspades_manual.html
+	http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+	http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE=""
 
 DEPEND="
@@ -28,6 +28,26 @@ DEPEND="
 	dev-libs/boost"
 RDEPEND="${DEPEND}"
 
+# 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
+# bwa-0.7.12
+# bwa-0.6.2
+
 pkg_pretend() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
 		if [[ $(tc-getCXX) == *g++ ]] ; then
@@ -39,13 +59,22 @@ pkg_pretend() {
 	fi
 }
 
-#src_compile(){
-#	# grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts
-#	PREFIX="${D}"/usr ./spades_compile.sh || die
-#}
+src_prepare(){
+	# https://github.com/Homebrew/homebrew-science/pull/5616
+	epatch "${FILESDIR}"/"${P}"-fix-missing-include.patch
+	cp -p spades_compile.sh spades_install.sh || die
+	sed -e 's/make install/#make install/;s/cd $PREFIX/#cd $PREFIX/' -i spades_compile.sh || die
+	default
+}
+
+src_compile(){
+	# grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts
+	PREFIX="${D}"/usr ./spades_compile.sh || die
+}
 
 src_install(){
-	PREFIX="${ED}"/usr ./spades_compile.sh || die
+	PREFIX="${ED}"/usr sh ./spades_install.sh || die
+	# BUG: move *.py files to standard site-packages/ subdirectories
 	insinto /usr/share/"${PN}"
 	dodoc "${DISTDIR}"/${P}_*manual.html
 }

diff --git a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
new file mode 100644
index 000000000..bb6d75797
--- /dev/null
+++ b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
@@ -0,0 +1,10 @@
+--- SPAdes-3.10.1/src/common/utils/segfault_handler.hpp.ori	2017-05-13 22:43:01.296207276 +0200
++++ SPAdes-3.10.1/src/common/utils/segfault_handler.hpp	2017-05-13 22:43:41.437310225 +0200
+@@ -12,6 +12,7 @@
+ #include "boost/noncopyable.hpp"
+ 
+ #include <signal.h>
++#include <functional>
+ 
+ struct segfault_handler : boost::noncopyable {
+     typedef std::function<void()> callback_t;

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

[Horea Christian]

commit:     dd4ee9b222cf98145af87c7ca36dc3d0e40cd8c0
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 17:59:43 2024 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 17:59:43 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dd4ee9b2

sci-biology/SPAdes: keyword 3.15.5 for ~amd64

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/SPAdes/SPAdes-3.15.5.ebuild            |  8 ++--
 sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch | 49 ++++++++++++++++++++++
 2 files changed, 54 insertions(+), 3 deletions(-)

diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
index b6d344c37..4485619e3 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -17,9 +17,7 @@ SRC_URI="
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS=""
-# Fails to build:
-# https://github.com/ablab/spades/issues/1238
+KEYWORDS="~amd64"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 DEPEND="
@@ -31,6 +29,10 @@ DEPEND="
 RDEPEND="${DEPEND}"
 BDEPEND="dev-build/cmake"
 
+PATCHES=(
+	"${FILESDIR}/${P}-gcc13.patch"
+)
+
 src_install(){
 	einstalldocs
 	# WORKAROUND: This script does both compile and install in one go

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"
+ 
+ /**