blob: 987fb99f2aeea40e33c0824fc84b42367c7d34ac (
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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
|
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python3_{7,8,9} )
inherit java-pkg-2 perl-module python-r1
DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
HOMEPAGE="https://canu.readthedocs.io/en/latest"
SRC_URI="https://github.com/marbl/canu/releases/download/v${PV}/${P}.tar.xz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
>=virtual/jre-1.8:*
dev-lang/perl
virtual/perl-File-Path
sci-visualization/gnuplot
sci-biology/minimap2
"
# =sci-biology/mhap-2.1.3 if we unbundle it
DEPEND="${RDEPEND}
>=virtual/jdk-1.8:*
dev-java/ant-core
"
# Detected file collision(s):
# * sci-biology/wgs-assembler-8.3_rc2:0::science
# * /usr/bin/bogart
# * /usr/bin/bogus
# * /usr/bin/fastqAnalyze
# * /usr/bin/fastqSample
# * /usr/bin/fastqSimulate
# * /usr/bin/fastqSimulate-sort
# * /usr/bin/meryl
# * /usr/bin/overlapInCore
# * /usr/bin/utgcns
# Perl 5.12.0, or File::Path 2.08
# Java SE 8
# https://github.com/marbl/MHAP uses Apache maven
# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON
src_compile(){
cd src || die
emake
}
src_install(){
# installs
# /usr/bin
# /usr/lib/libcanu.a
# /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu
# /usr/share/java/classes/mhap-2.1.3.jar
rm -rf Linux-amd64/obj
insinto /usr
doins -r Linux-amd64/{bin,share}
insinto /usr/$(get_libdir)
dolib.a Linux-amd64/lib/libcanu.a
rm Linux-amd64/lib/libcanu.a || die
perl_set_version
perl_domodule -r Linux-amd64/lib
}
|
GitWeb
