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
|
# Copyright 2013-2019 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 *
import glob
class Redundans(Package):
"""Redundans pipeline assists an assembly of heterozygous genomes."""
homepage = "https://github.com/Gabaldonlab/redundans"
url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
git = "https://github.com/Gabaldonlab/redundans.git"
version('0.14a', commit='a20215a862aed161cbfc79df9133206156a1e9f0')
version('0.13c', sha256='26d48f27a32678d94c1d00cb3b8991d74891d6cad64a94569901ff9607a7a736')
depends_on('python', type=('build', 'run'))
depends_on('py-pyscaf', type=('build', 'run'))
depends_on('py-fastaindex', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('perl', type=('build', 'run'))
depends_on('sspace-standard')
depends_on('bwa')
depends_on('last')
depends_on('gapcloser')
depends_on('parallel')
depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))
def install(self, spec, prefix):
sspace_location = join_path(spec['sspace-standard'].prefix,
'SSPACE_Standard_v3.0.pl')
filter_file(r'sspacebin = os.path.join(.*)$',
'sspacebin = \'' + sspace_location + '\'',
'redundans.py')
binfiles = ['redundans.py', 'bin/filterReads.py']
binfiles.extend(glob.glob('bin/fast?2*.py'))
# new internal dep with 0.14a
if spec.satisfies('@0.14a:'):
binfiles.append('bin/denovo.py')
mkdirp(prefix.bin)
for f in binfiles:
install(f, prefix.bin)
|
