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
71
72
|
##############################################################################
# Copyright (c) 2013-2018, 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 *
from shutil import copyfile
import glob
import os.path
import re
class Gatk(Package):
"""Genome Analysis Toolkit
Variant Discovery in High-Throughput Sequencing Data
"""
homepage = "http://broadinstitute.github.io/gatk/"
url = "https://software.broadinstitute.org/gatk/download/auth?package=GATK"
_urlfmt = "https://github.com/broadgsa/gatk-protected/archive/{0}.tar.gz"
version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
depends_on('java@8:', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
# The list of files to install varies with release...
# ... but skip the spack-{build.env}.out files.
files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
for f in files:
install(f, prefix.bin)
# Set up a helper script to call java on the jar file,
# explicitly codes the path for java and the jar file.
script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
script = join_path(prefix.bin, "gatk")
copyfile(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
java = join_path(self.spec['java'].prefix, 'bin', 'java')
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file('GenomeAnalysisTK.jar', join_path(prefix.bin,
'GenomeAnalysisTK.jar'),
script, **kwargs)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('GATK',
join_path(self.prefix, 'bin',
'GenomeAnalysisTK.jar'))
|
