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

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

[Martin Mokrejs]

commit:     e13abc54d0a4bb65bdb67109fbe1ee61f401cf88
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 21:21:00 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 21:21:00 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e13abc54

sci-biology/megahit: new package

Package-Manager: portage-2.2.28

 sci-biology/megahit/megahit-9999.ebuild | 34 +++++++++++++++++++++++++++++++++
 sci-biology/megahit/metadata.xml        | 12 ++++++++++++
 2 files changed, 46 insertions(+)

diff --git a/sci-biology/megahit/megahit-9999.ebuild b/sci-biology/megahit/megahit-9999.ebuild
new file mode 100644
index 0000000..def7fd6
--- /dev/null
+++ b/sci-biology/megahit/megahit-9999.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit git-r3 toolchain-funcs
+
+DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with CUDA"
+HOMEPAGE="https://github.com/voutcn/megahit
+	http://bioinformatics.oxfordjournals.org/content/31/10/1674.abstract"
+EGIT_REPO_URI="https://github.com/voutcn/megahit.git"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE="+openmp"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sys-libs/zlib"
+# >=gcc-4.4
+
+# use make use_gpu=1 to compile it and turn on --use-gpu to activate GPU acceleration when running megahit
+
+src_prepare(){
+	default
+	sed -e "s#^CXXFLAGS = -g -O2#CXXFLAGS = ${CFLAGS}#" -i Makefile || die
+}
+
+src_install(){
+	dobin megahit megahit_toolkit megahit_sdbg_build megahit_asm_core
+	dodoc README.md
+}

diff --git a/sci-biology/megahit/metadata.xml b/sci-biology/megahit/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/megahit/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

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

[Martin Mokrejs]

commit:     cbe0d928b5c7dbe615e129da4d5079f46324aef8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 01:00:37 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 01:00:37 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cbe0d928

sci-biology/megahit: distinguish openmp compiler switches

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/megahit/megahit-9999.ebuild | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/sci-biology/megahit/megahit-9999.ebuild b/sci-biology/megahit/megahit-9999.ebuild
index def7fd6..a23d2c2 100644
--- a/sci-biology/megahit/megahit-9999.ebuild
+++ b/sci-biology/megahit/megahit-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -23,8 +23,20 @@ RDEPEND="${DEPEND}
 
 # use make use_gpu=1 to compile it and turn on --use-gpu to activate GPU acceleration when running megahit
 
+pkg_setup() {
+	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
 src_prepare(){
 	default
+	if [[ $(tc-getCXX) =~ g++ ]]; then
+		local eopenmp=-fopenmp
+	elif [[ $(tc-getCXX) =~ cxx ]]; then
+		local eopenmp=-openmp
+		sed -e "s#-fopenmp#-openmp#" -i Makefile || die
+	else
+		elog "Cannot detect compiler type so not setting openmp support"
+	fi
 	sed -e "s#^CXXFLAGS = -g -O2#CXXFLAGS = ${CFLAGS}#" -i Makefile || die
 }
 

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

[Martin Mokrejs]

commit:     42f362924ffcccf2cecfbd18f52bbb7eabf9f28e
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 22:34:23 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 22:34:23 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=42f36292

sci-biology/megahit: respect cuda USE flag

Package-Manager: Portage-2.3.31, Repoman-2.3.9

 sci-biology/megahit/megahit-9999.ebuild | 27 +++++++++++++++++++++------
 sci-biology/megahit/metadata.xml        |  3 +++
 2 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/sci-biology/megahit/megahit-9999.ebuild b/sci-biology/megahit/megahit-9999.ebuild
index 2fd8fa242..e403604ca 100644
--- a/sci-biology/megahit/megahit-9999.ebuild
+++ b/sci-biology/megahit/megahit-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit git-r3 toolchain-funcs
+inherit git-r3 toolchain-funcs eutils
 
 DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with CUDA"
 HOMEPAGE="https://github.com/voutcn/megahit
@@ -13,14 +13,14 @@ EGIT_REPO_URI="https://github.com/voutcn/megahit.git"
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS=""
-IUSE="+openmp"
+IUSE="+openmp cuda"
 
 DEPEND=""
 RDEPEND="${DEPEND}
-	sys-libs/zlib"
+	sys-libs/zlib
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-5 dev-libs/cudnn )"
 # >=gcc-4.4
-
-# use make use_gpu=1 to compile it and turn on --use-gpu to activate GPU acceleration when running megahit
+# contains bundled copy og idba from https://github.com/loneknightpy/idba
 
 pkg_setup() {
 	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
@@ -36,10 +36,25 @@ src_prepare(){
 	else
 		elog "Cannot detect compiler type so not setting openmp support"
 	fi
+	if use cuda; then
+		local makeopts="use_gpu=1"
+	else
+		local makeopts=""
+	fi
 	sed -e "s#^CXXFLAGS = -g -O2#CXXFLAGS = ${CFLAGS}#" -i Makefile || die
 }
 
+src_compile(){
+	emake $makeopts
+}
+
 src_install(){
 	dobin megahit megahit_toolkit megahit_sdbg_build megahit_asm_core
 	dodoc README.md
 }
+
+pkg_postinst(){
+	einfo "The maximum k-mer size is 255. You can edit kMaxK in definitions.h"
+	einfo "and recompile, eventually"
+	einfo "If you enabled GPU then use 'megahit --use-gpu' to activate it."
+}

diff --git a/sci-biology/megahit/metadata.xml b/sci-biology/megahit/metadata.xml
index bbab8b46d..a4779f691 100644
--- a/sci-biology/megahit/metadata.xml
+++ b/sci-biology/megahit/metadata.xml
@@ -12,4 +12,7 @@
 	<upstream>
 		<remote-id type="github">voutcn/megahit</remote-id>
 	</upstream>
+	<use>
+		<flag name="cuda">Enable NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5</flag>
+	</use>
 </pkgmetadata>

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

[Andrew Ammerlaan]

commit:     1fde48bc8a281488cb15029775ef42ba9d918d5f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 12:17:41 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 12:17:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1fde48bc

sci-biology/megahit: EAPI bump, fix build

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../{megahit-9999.ebuild => megahit-1.2.9.ebuild}  | 38 +++-------------------
 1 file changed, 5 insertions(+), 33 deletions(-)

diff --git a/sci-biology/megahit/megahit-9999.ebuild b/sci-biology/megahit/megahit-1.2.9.ebuild
similarity index 52%
rename from sci-biology/megahit/megahit-9999.ebuild
rename to sci-biology/megahit/megahit-1.2.9.ebuild
index e403604ca..3e1766259 100644
--- a/sci-biology/megahit/megahit-9999.ebuild
+++ b/sci-biology/megahit/megahit-1.2.9.ebuild
@@ -1,58 +1,30 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit git-r3 toolchain-funcs eutils
+inherit toolchain-funcs cmake
 
 DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with CUDA"
 HOMEPAGE="https://github.com/voutcn/megahit
 	http://bioinformatics.oxfordjournals.org/content/31/10/1674.abstract"
-EGIT_REPO_URI="https://github.com/voutcn/megahit.git"
+SRC_URI="https://github.com/voutcn/megahit/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE="+openmp cuda"
 
 DEPEND=""
 RDEPEND="${DEPEND}
 	sys-libs/zlib
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-5 dev-libs/cudnn )"
-# >=gcc-4.4
 # contains bundled copy og idba from https://github.com/loneknightpy/idba
 
 pkg_setup() {
 	use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
 }
 
-src_prepare(){
-	default
-	if [[ $(tc-getCXX) =~ g++ ]]; then
-		local eopenmp=-fopenmp
-	elif [[ $(tc-getCXX) =~ cxx ]]; then
-		local eopenmp=-openmp
-		sed -e "s#-fopenmp#-openmp#" -i Makefile || die
-	else
-		elog "Cannot detect compiler type so not setting openmp support"
-	fi
-	if use cuda; then
-		local makeopts="use_gpu=1"
-	else
-		local makeopts=""
-	fi
-	sed -e "s#^CXXFLAGS = -g -O2#CXXFLAGS = ${CFLAGS}#" -i Makefile || die
-}
-
-src_compile(){
-	emake $makeopts
-}
-
-src_install(){
-	dobin megahit megahit_toolkit megahit_sdbg_build megahit_asm_core
-	dodoc README.md
-}
-
 pkg_postinst(){
 	einfo "The maximum k-mer size is 255. You can edit kMaxK in definitions.h"
 	einfo "and recompile, eventually"