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
|
##############################################################################
# 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 os.path
class Haploview(Package):
"""Haploview is designed to simplify and expedite the process of haplotype
analysis."""
homepage = "http://www.broadinstitute.org/haploview/haploview"
url = "https://downloads.sourceforge.net/project/haploview/release/Haploview4.1.jar"
version('4.1', 'f7aa4accda5fad1be74c9c1969c6ee7d', expand=False)
depends_on('java', type=('build', 'run'))
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'Haploview{v}.jar'.format(v=self.version)
install(jar_file, prefix.bin)
script_sh = join_path(os.path.dirname(__file__), "haploview.sh")
script = prefix.bin.haploview
install(script_sh, script)
set_executable(script)
java = self.spec['java'].prefix.bin.java
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file('haploview.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
|
