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
|
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Freebayes(MesonPackage):
"""Bayesian haplotype-based genetic polymorphism discovery and
genotyping."""
homepage = "https://github.com/ekg/freebayes"
url = "https://github.com/freebayes/freebayes/releases/download/v1.3.5/freebayes-1.3.5-src.tar.gz"
git = "https://github.com/ekg/freebayes.git"
version('1.3.5', sha256='7e2635690e916ed85cec36b3263e6e5357413a4f2bf3035362d9749335e8a696')
version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
submodules=True, deprecated=True)
depends_on('cmake', type='build')
depends_on('zlib')
# Deps for @1.3.5 and beyond
depends_on('ninja', type='build', when='@1.3.5:')
depends_on('htslib', when='@1.3.5:')
depends_on('zlib', when='@1.3.5:')
depends_on('xz', when='@1.3.5:')
depends_on('parallel', when='@1.3.5:')
depends_on('vcftools', when='@1.3.5:')
depends_on('bc', when='@1.3.5:')
depends_on('samtools', when='@1.3.5:')
parallel = False
@when('@:1.1.0')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
b = prefix.bin
makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/',
'cp bin/freebayes bin/bamleftalign {0}'.format(b))
@when('@:1.1.0')
@run_before('install')
def make_prefix_dot_bin(self):
mkdir(prefix.bin)
@when('@:1.1.0')
def meson(self, spec, prefix):
pass
@when('@:1.1.0')
def build(self, spec, prefix):
make()
@when('@:1.1.0')
def install(self, spec, prefix):
make('install')
|
