commit: 86dd71ff4e5aaf1d07e78b746045ec800fe2bafe Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Feb 1 08:12:20 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Mon Feb 1 08:12:20 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=86dd71ff
sci-biology/SOAPdenovo2: version bump 242 no keywords yet, because it does not compile Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> ...APdenovo2-241.ebuild => SOAPdenovo2-242.ebuild} | 31 +++++++++------------- 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild similarity index 51% rename from sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild rename to sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild index e3679664d..8ae80d466 100644 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild +++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild @@ -1,19 +1,18 @@ -# 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 toolchain-funcs eutils +inherit toolchain-funcs DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)" HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2 - http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"; -SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r241.tar.gz -> ${P}.tar.gz" + https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"; +SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -KEYWORDS="" -IUSE="" +KEYWORDS="" # fails to compile DEPEND="dev-libs/libaio sci-biology/samtools:0.1-legacy" @@ -22,7 +21,7 @@ RDEPEND="${DEPEND}" S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241 src_prepare(){ - epatch "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch + #eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch # this will be partly covered by # https://github.com/aquaskyline/SOAPdenovo2/pull/44 # @@ -33,15 +32,11 @@ src_prepare(){ sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \ standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \ sparsePregraph/*.a || die + find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die + find -type f -name "*.h" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die + find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die + find -type f -name "*.c*" -exec sed -i -e 's/#include "bam.h"/#include "bam-0.1-legacy\/bam.h"/g' {} + || die + find -type f -name "*.c*" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die + find -type f -name "*.c*" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die default } - -src_compile(){ - cd standardPregraph && emake -j1 63mer=1 - cd ../standardPregraph && emake -j1 127mer=1 - cd ../sparsePregraph && emake -j1 -} - -src_install(){ - doman "${FILESDIR}"/SOAPdenovo2.1 -}
