[gentoo-commits] proj/sci:master commit in: sci-biology/megahit/
commit: 1fde48bc8a281488cb15029775ef42ba9d918d5f
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 12:17:41 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 12:17:41 2021 +
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 riseup.net>
.../{megahit-.ebuild => megahit-1.2.9.ebuild} | 38 +++---
1 file changed, 5 insertions(+), 33 deletions(-)
diff --git a/sci-biology/megahit/megahit-.ebuild
b/sci-biology/megahit/megahit-1.2.9.ebuild
similarity index 52%
rename from sci-biology/megahit/megahit-.ebuild
rename to sci-biology/megahit/megahit-1.2.9.ebuild
index e403604ca..3e1766259 100644
--- a/sci-biology/megahit/megahit-.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 $makeopts
-}
-
-src_install(){
- dobin megahit megahit_toolkit megahit_sdbg_build megahit_asm_core
- dodoc README.md
-}
-
pkg_postinst(){
einfo "The maximum k-mer size is 255. You can edit kMaxK in
definitions.h"
einfo "and recompile, eventually"
[gentoo-commits] proj/sci:master commit in: sci-biology/megahit/
commit: 42f362924ffcccf2cecfbd18f52bbb7eabf9f28e
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sun Apr 22 22:34:23 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 22 22:34:23 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=42f36292
sci-biology/megahit: respect cuda USE flag
Package-Manager: Portage-2.3.31, Repoman-2.3.9
sci-biology/megahit/megahit-.ebuild | 27 +--
sci-biology/megahit/metadata.xml| 3 +++
2 files changed, 24 insertions(+), 6 deletions(-)
diff --git a/sci-biology/megahit/megahit-.ebuild
b/sci-biology/megahit/megahit-.ebuild
index 2fd8fa242..e403604ca 100644
--- a/sci-biology/megahit/megahit-.ebuild
+++ b/sci-biology/megahit/megahit-.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-inherit git-r3 toolchain-funcs
+inherit git-r3 toolchain-funcs eutils
DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with
CUDA"
HOMEPAGE="https://github.com/voutcn/megahit
@@ -13,14 +13,14 @@ EGIT_REPO_URI="https://github.com/voutcn/megahit.git;
LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
-IUSE="+openmp"
+IUSE="+openmp cuda"
DEPEND=""
RDEPEND="${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 @@
voutcn/megahit
+
+ Enable NVIDIA GTX680 (4G memory) and Tesla
K40c (12G memory) with CUDA 5.5, 6.0 and 6.5
+
[gentoo-commits] proj/sci:master commit in: sci-biology/megahit/
commit: cbe0d928b5c7dbe615e129da4d5079f46324aef8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 10 01:00:37 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 10 01:00:37 2017 +
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-.ebuild | 14 +-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/sci-biology/megahit/megahit-.ebuild
b/sci-biology/megahit/megahit-.ebuild
index def7fd6..a23d2c2 100644
--- a/sci-biology/megahit/megahit-.ebuild
+++ b/sci-biology/megahit/megahit-.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/
commit: e13abc54d0a4bb65bdb67109fbe1ee61f401cf88
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Apr 10 21:21:00 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 10 21:21:00 2016 +
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-.ebuild | 34 +
sci-biology/megahit/metadata.xml| 12
2 files changed, 46 insertions(+)
diff --git a/sci-biology/megahit/megahit-.ebuild
b/sci-biology/megahit/megahit-.ebuild
new file mode 100644
index 000..def7fd6
--- /dev/null
+++ b/sci-biology/megahit/megahit-.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 000..f68a1b6
--- /dev/null
+++ b/sci-biology/megahit/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
