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
|
# Copyright 2013-2024 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)
import glob
import os.path
import re
from spack.package import *
class Picard(Package):
"""Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
"""
homepage = "https://broadinstitute.github.io/picard/"
url = "https://github.com/broadinstitute/picard/releases/download/2.26.2/picard.jar"
_urlfmt = "https://github.com/broadinstitute/picard/releases/download/{0}/picard.jar"
_oldurlfmt = (
"https://github.com/broadinstitute/picard/releases/download/{0}/picard-tools-{0}.zip"
)
license("GPL-2.0-or-later")
# They started distributing a single jar file at v2.6.0, prior to
# that it was a .zip file with multiple .jar and .so files
version(
"3.0.0",
sha256="0d5e28ab301fad3b02030d01923888129ba82c5f722ac5ccb2d418ab76ac5499",
expand=False,
)
version(
"2.26.2",
sha256="99fab1699a735fd048a05975a243774f1cc99e87a9b28311d4aa872d06390474",
expand=False,
)
version(
"2.25.7",
sha256="dc0e830d3e838dee2b4f4aa1c9631fb3a4c3ec982de8dfe5145fc748104c7146",
expand=False,
)
version(
"2.25.6",
sha256="768709826514625381e6fa3920945360167f4e830bf72f79eb070da059676f02",
expand=False,
)
version(
"2.25.5",
sha256="f7fa9784b84d384abfcbd77076f5ceab7b2797dc863ac35fd41470daa3efe3a5",
expand=False,
)
version(
"2.25.4",
sha256="c3ac14471e48e28e24201ae5515f828ffa45db7ac3e37173251a672845b4a9b3",
expand=False,
)
version(
"2.25.3",
sha256="1d4dbfcb36d23fde11f173ab0de8a99835e04161efb04f246bbcbfc0bee3b493",
expand=False,
)
version(
"2.25.2",
sha256="aead4baf12028a5d2b9ef70e00c93e4bba8f6bece0b9a7104b89b842a8e0326f",
expand=False,
)
version(
"2.25.1",
sha256="6d6e622d6b465f9fc704c37bcba55b0dac5ad14d07088bbdbdfade5cd027ee1c",
expand=False,
)
version(
"2.25.0",
sha256="faf2434da84fe21b516d57817767920fdedfc19ebdc01d9cae8d6d3314f7e897",
expand=False,
)
version(
"2.24.0",
sha256="70e91039bccc6f6db60f18c41713218a8cdf45f591f02c1012c062152b27cd7b",
expand=False,
)
version(
"2.20.8",
sha256="aff92d618ee9e6bafc1ab4fbfa89fc557a0dbe596ae4b92fe3bf93ebf95c7105",
expand=False,
)
version(
"2.19.0",
sha256="f97fc3f7a73b55cceea8b6a6488efcf1b2fbf8cad61d88645704ddd45a8c5950",
expand=False,
)
version(
"2.18.3",
sha256="0e0fc45d9a822ee9fa562b3bb8f1525a439e4cd541429a1a4ca4646f37189b70",
expand=False,
)
version(
"2.18.0",
sha256="c4c64b39ab47968e4afcaf1a30223445ee5082eab31a03eee240e54c2e9e1dce",
expand=False,
)
version(
"2.17.0",
sha256="ffea8bf90e850919c0833e9dcc16847d40090a1ef733c583a710a3282b925998",
expand=False,
)
version(
"2.16.0",
sha256="01cf3c930d2b4841960497491512d327bf669c1ed2e753152e1e651a27288c2d",
expand=False,
)
version(
"2.15.0",
sha256="dc3ff74c704954a10796b390738078617bb0b0fef15731e9d268ed3b26c6a285",
expand=False,
)
version(
"2.13.2",
sha256="db7749f649e8423053fb971e6af5fb8a9a1a797cb1f20fef1100edf9f82f6f94",
expand=False,
)
version(
"2.10.0",
sha256="e256d5e43656b7d8be454201a7056dce543fe9cbeb30329a0d8c22d28e655775",
expand=False,
)
version(
"2.9.4",
sha256="0ecee9272bd289d902cc18053010f0364d1696e7518ac92419a99b2f0a1cf689",
expand=False,
)
version(
"2.9.3",
sha256="6cca26ce5094b25a82e1a8d646920d584c6db5f009476196dc285be6522e00ce",
expand=False,
)
version(
"2.9.2",
sha256="05714b9743a7685a43c94a93f5d03aa4070d3ab6e20151801301916d3e546eb7",
expand=False,
)
version(
"2.9.0",
sha256="9a57f6bd9086ea0f5f1a6d9d819459854cb883bb8093795c916538ed9dd5de64",
expand=False,
)
version(
"2.8.3",
sha256="97a4b6c8927c8cb5f3450630c9b39bf210ced8c271f198119118ce1c24b8b0f6",
expand=False,
)
version(
"2.6.0",
sha256="671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b",
expand=False,
)
version("1.140", sha256="0d27287217413db6b846284c617d502eaa578662dcb054a7017083eab9c54438")
variant("parameters", default=False, description="get java parameters in the adapter script")
depends_on("java@17:", type="run", when="@3.0.0:")
depends_on("java@8:", type="run", when="@:2.27.5")
def install(self, spec, prefix):
mkdirp(prefix.bin)
# The list of files to install varies with release...
# ... but skip the spack-build-{env}out.txt 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__),
"picard_with_parameters.sh" if "+parameters" in spec else "picard.sh",
)
script = prefix.bin.picard
install(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
java = self.spec["java"].prefix.bin.java
kwargs = {"ignore_absent": False, "backup": False, "string": False}
filter_file("^java", java, script, **kwargs)
filter_file("picard.jar", join_path(prefix.bin, "picard.jar"), script, **kwargs)
def setup_run_environment(self, env):
"""The Picard docs suggest setting this as a convenience."""
env.prepend_path("PICARD", join_path(self.prefix.bin, "picard.jar"))
def url_for_version(self, version):
if version < Version("2.6.0"):
return self._oldurlfmt.format(version)
else:
return self._urlfmt.format(version)
|
