blob: 0ca68007af43074821cdfd850def3975187c3fca (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit toolchain-funcs
DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph)"
HOMEPAGE="https://sourceforge.net/projects/soapdenovo2
https://github.com/aquaskyline/SOAPdenovo2
http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
SRC_URI="https://sourceforge.net/projects/soapdenovo2/files/${PN}/src/r${PV}/${PN}-src-r${PV}.tgz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="dev-libs/libaio
sci-biology/samtools:0.1-legacy"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/"${PN}"-src-r"${PV}" # version is 2.04-r240
src_prepare(){
# pass to broken Makefile's a proper C++ compiler through the CC variable
sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i Makefile || die
sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i Makefile || die
sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i sparsePregraph/Makefile || die
sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i sparsePregraph/Makefile || die
rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \
sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
sparsePregraph/*.a || die
default
}
src_compile(){
cd standardPregraph && emake -j1 63mer=1
cd ../standardPregraph && emake -j1 127mer=1
cd ../sparsePregraph && emake -j1
}
src_install(){
doman "${FILESDIR}"/SOAPdenovo2.1
}
|
GitWeb
