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
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
|
##############################################################################
# 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
##############################################################################
#
# This is a based largely on the Homebrew science formula:
# https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
#
# There s one tricky bit to be resolved:
#
# - HDF5 builds explode, blast's configure script tries to run a program that
# uses a variable called 'HOST' but some other bit defines a macro called
# HOST that's defined to a string. Hilarity ensues.
#
#
from spack import *
class BlastPlus(AutotoolsPackage):
"""Basic Local Alignment Search Tool."""
homepage = "http://blast.ncbi.nlm.nih.gov/"
url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
version('2.6.0', 'c8ce8055b10c4d774d995f88c7cc6225')
version('2.2.30', 'f8e9a5eb368173142fe6867208b73715')
# homebrew sez: Fixed upstream in future version > 2.6
# But this bug sez that it will be fixed in 2.6
# https://github.com/Homebrew/homebrew-science/pull/4740
# The 2.6.0 src still matches the "before" bit of the patch
# so it's probably still "needed".
# On the other hand, the `find` command is broken and there
# aren't any .svn dirs in the tree, so I've updated their patch
# to just comment out the block.
patch('blast-make-fix2.5.0.diff', when="@2.5.0:2.6.0")
# See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511
@when('@:2.2.31')
def patch(self):
filter_file("2.95* | 2.96* | 3.* | 4.* )",
"2.95* | 2.96* | 3.* | 4.* | 5.* )",
"c++/src/build-system/configure",
string=True)
# No...
# depends_on :mysql => :optional
variant('static', default=False,
description='Build with static linkage')
variant('jpeg', default=True,
description='Build with jpeg support')
variant('png', default=True,
description='Build with png support')
variant('freetype', default=True,
description='Build with freetype support')
# variant('hdf5', default=True,
# description='Build with hdf5 support')
variant('gnutls', default=True,
description='Build with gnutls support')
variant('openssl', default=True,
description='Build with openssl support')
variant('zlib', default=True,
description='Build with zlib support')
variant('bzip2', default=True,
description='Build with bzip2 support')
variant('lzo', default=True,
description='Build with lzo support')
variant('pcre', default=True,
description='Build with pcre support')
variant('perl', default=True,
description='Build with perl support')
variant('python', default=True,
description='Build with python support')
depends_on('jpeg', when='+jpeg')
depends_on('libpng', when='+png')
depends_on('freetype', when='+freetype')
# depends_on('hdf5', when='+hdf5')
depends_on('gnutls', when='+gnutls')
depends_on('openssl', when='+openssl')
depends_on('zlib', when='+zlib')
depends_on('bzip2', when='+bzip2')
depends_on('lzo', when='+lzo')
depends_on('pcre', when='+pcre')
depends_on('python', when='+python')
depends_on('perl', when='+perl')
configure_directory = 'c++'
def configure_args(self):
spec = self.spec
config_args = [
'--with-bin-release',
'--without-debug',
'--with-mt',
'--with-64',
'--without-boost',
]
if '+static' in spec:
config_args.append('--with-static')
# FIXME
# args << "--with-static-exe" unless OS.linux?
# args << "--with-dll" if build.with? "dll"
else:
config_args.extend([
'--with-dll',
'--without-static',
'--without-static-exe'
])
if '+jpeg' in spec:
config_args.append(
'--with-jpeg={0}'.format(self.spec['jpeg'].prefix)
)
else:
config_args.append('--without-jpeg')
if '+png' in spec:
config_args.append(
'--with-png={0}'.format(self.spec['libpng'].prefix)
)
else:
config_args.append('--without-png')
if '+freetype' in spec:
config_args.append(
'--with-freetype={0}'.format(self.spec['freetype'].prefix)
)
else:
config_args.append('--without-freetype')
config_args.append('--without-hdf5')
# if '+hdf5' in spec:
# # FIXME
# config_args.append(
# '--with-hdf5={0}'.format(self.spec['hdf5'].prefix)
# )
# else:
# config_args.append('--without-hdf5')
if '+zlib' in spec:
config_args.append(
'--with-z={0}'.format(self.spec['zlib'].prefix)
)
else:
config_args.append('--without-z')
if '+bzip2' in spec:
config_args.append(
'--with-bz2={0}'.format(self.spec['bzip2'].prefix)
)
else:
config_args.append('--without-bz2')
if '+lzo' in spec:
config_args.append(
'--with-lzo={0}'.format(self.spec['lzo'].prefix)
)
else:
config_args.append('--without-lzo')
if '+gnutls' in spec:
config_args.append(
'--with-gnutls={0}'.format(self.spec['gnutls'].prefix)
)
else:
config_args.append('--without-gnutls')
if '+openssl' in spec:
config_args.append(
'--with-openssl={0}'.format(self.spec['openssl'].prefix)
)
else:
config_args.append('--without-openssl')
if '+pcre' in spec:
config_args.append(
'--with-pcre={0}'.format(self.spec['pcre'].prefix)
)
else:
config_args.append('--without-pcre')
if '+python' in spec:
config_args.append(
'--with-python={0}'.format(self.spec['python'].home)
)
else:
config_args.append('--without-python')
if '+perl' in spec:
config_args.append(
'--with-perl={0}'.format(self.spec['perl'].prefix)
)
else:
config_args.append('--without-python')
return config_args
|
