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
|
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import glob
import os
class Kraken(Package):
"""Kraken is a system for assigning taxonomic labels to short DNA
sequences, usually obtained through metagenomic studies."""
homepage = "https://ccb.jhu.edu/software/kraken/"
url = "https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz"
version('1.0', 'e790d6b09662bbd810aa34517ef66586')
depends_on('perl', type=('build', 'run'))
# Does NOT support JELLYFISH 2.0. Ver 1.1.11 is the last version of
# JELLYFISH 1.
depends_on('jellyfish@1.1.11', when='@1.0')
def install(self, spec, prefix):
installer = Executable('./install_kraken.sh')
installer(self.stage.source_path)
mkdirp(prefix.bin)
files = glob.iglob('*')
for file in files:
if os.path.isfile(file):
install(file, prefix.bin)
|
