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>
