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"
