From 86dd71ff4e5aaf1d07e78b746045ec800fe2bafe Mon Sep 17 00:00:00 2001 From: Andrew Ammerlaan Date: Mon, 1 Feb 2021 09:12:20 +0100 Subject: 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 --- sci-biology/SOAPdenovo2/Manifest | 2 +- sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild | 47 -------------------------- sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild | 42 +++++++++++++++++++++++ 3 files changed, 43 insertions(+), 48 deletions(-) delete mode 100644 sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild create mode 100644 sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild (limited to 'sci-biology/SOAPdenovo2') diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest index 047465b7e..f732ff7a8 100644 --- a/sci-biology/SOAPdenovo2/Manifest +++ b/sci-biology/SOAPdenovo2/Manifest @@ -1 +1 @@ -DIST SOAPdenovo2-241.tar.gz 1532760 BLAKE2B 3229ca63b8ecb5012cc8eaa16991ea1385c63da1d7b78c8a3ade6b5fe0b90be08c08d18d3f5e5d708e3af50d5a06e9413807b00e6512965fbc2b8b07ec2dcc6b SHA512 7b0cd992e437f9e5c6f4878c3d3b1fa93f3f8aa3d40895f88cc7a99f7cd69003c4db4d27d7aaa1c2f9f43741f048a74c2479aced44ce4b9432405195749af2e2 +DIST SOAPdenovo2-242.tar.gz 1534059 BLAKE2B e72b8b8005a807e1f949d092a1b582ed75ddbd3f4a1f014f86754ae69e279b93758693f36942e16183095fcfcc843a637fab39b08cfa6b8cbeffaf8b07c3050a SHA512 eaa2020aa9054588805bd69bb2e1d70be5bfcad31d52a33ed8f7accd4006db1ec980b20f846a6e1c0ee0ec8a493c38febb9022ce6a59c14d03fe43a3ca50569b diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild deleted file mode 100644 index e3679664d..000000000 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs eutils - -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 -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="dev-libs/libaio - sci-biology/samtools:0.1-legacy" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241 - -src_prepare(){ - epatch "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch - # this will be partly covered by - # https://github.com/aquaskyline/SOAPdenovo2/pull/44 - # - for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do - sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die - done - rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \ - sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \ - standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \ - sparsePregraph/*.a || die - default -} - -src_compile(){ - cd standardPregraph && emake -j1 63mer=1 - cd ../standardPregraph && emake -j1 127mer=1 - cd ../sparsePregraph && emake -j1 -} - -src_install(){ - doman "${FILESDIR}"/SOAPdenovo2.1 -} diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild new file mode 100644 index 000000000..8ae80d466 --- /dev/null +++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)" +HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2 + https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18" +SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" # fails to compile + +DEPEND="dev-libs/libaio + sci-biology/samtools:0.1-legacy" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241 + +src_prepare(){ + #eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch + # this will be partly covered by + # https://github.com/aquaskyline/SOAPdenovo2/pull/44 + # + for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do + sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die + done + rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \ + 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 +} -- cgit v1.2.3-65-gdbad