diff options
Diffstat (limited to 'sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild')
| -rw-r--r-- | sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild | 42 |
1 files changed, 0 insertions, 42 deletions
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild deleted file mode 100644 index 8ae80d466..000000000 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# 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 -} |