-
Notifications
You must be signed in to change notification settings - Fork 40
/
config.yaml
415 lines (407 loc) · 12.4 KB
/
config.yaml
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
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
---
## Lines that must be updated when we release a new software version are
## indicated in comments below
output_dir: output
staging_deploy_root: [email protected]:/loc/www/bioconductor-test-new
production_deploy_root: [email protected]:/extra/www/bioc
staging_dir: /loc/www/bioconductor-test-new
## CHANGE THIS WHEN WE RELEASE A VERSION:
release_version: "3.20"
r_version_associated_with_release: "4.4.0"
r_version_associated_with_devel: "4.5.0"
## CHANGE THIS WHEN WE RELEASE A VERSION:
devel_version: "3.21"
## CHANGE THIS WHEN WE ADD A VERSION:
## This is the list of all versions for which we want to generate "new"
## bioc-views, package index, and package detail pages.
## if old versions (no older than 2.5) need to be rebuilt for any reason,
## add them here, but in most cases this should just contain the
## release and devel versions (though after a release you should
## let the no-longer-release version build one last time so package
## landing pages won't say "release version"):
versions:
- "3.20"
- "3.21"
## CHANGE THIS (i.e., uncomment) as various parts of the new devel version
## become available. set to "[]" if none are available.
devel_repos:
- "bioc"
- "data/experiment"
- "workflows"
- "data/annotation"
## CHANGE this when the build machines change:
## also, don't include machines that are not building yet (comment them out)
active_release_builders:
linux: "nebbiolo2"
windows: "palomino8"
mac_monterey: "lconway"
active_devel_builders:
linux: "nebbiolo1"
windows: "palomino7"
# mac_monterey: "merida1"
## CHANGE this when the single package builder builds
## on a newer version of bioc
single_package_builder:
bioc_version: "3.21"
r_version: "4.5"
rss_hub_url: "https://pubsubhubbub.appspot.com/"
## CHANGE these as AMI IDS change
ami_ids:
bioc2_8: ami-3a2ef452
bioc2_9: ami-2623f94e
bioc2_10: ami-5621fb3e
bioc2_11: ami-f827fd90
bioc2_12: ami-7224fe1a
bioc2_13: ami-4a25ff22
bioc2_14: ami-9c25fff4
bioc3_0: ami-be7917d6
bioc3_1: ami-a3d126c8
bioc3_2: ami-85d88de0
bioc3_3: ami-abd0b3bc
bioc3_4: ami-8946709f
bioc3_5: ami-279a315d
bioc3_6: ami-ac5df1d3
bioc3_7: ami-01bcd08e357360496
bioc3_8: ami-0565362d8bfb9cbed
bioc3_9: ami-0f5d1990d8c571cdf
bioc3_10: ami-0c5ab50ca03a54468
bioc3_11: ami-071b80cf0d8ca085c
bioc3_12: ami-04c69d122c1cf7e81
bioc3_13: ami-0e7efd11a6eab85a6
string_pattern_type: legacy
data_sources:
- items_root: /
layouts_root: /
type: filesystem_unified
identifier_type: legacy
encoding: utf-8
config:
encoding: utf-8
- items_root: /
type: biostar_list
identifier_type: legacy
encoding: utf-8
config:
gmane_rss_url: 'http://rss.gmane.org/messages/excerpts/gmane.science.biology.informatics.conductor'
cache_file: tmp/gmane_list_cache_file.yaml
encoding: utf-8
ttl: 10
- items_root: /help/bioc-views/package-pages
layouts_root: /
type: bioc_views
identifier_type: legacy
encoding: utf-8
config:
json_dir: "assets/packages/json"
encoding: utf-8
- items_root: /help/publications/papers/pubmed
type: pubmed_papers
identifier_type: legacy
encoding: utf-8
config:
cache_file: tmp/pubmed_cache_file.yaml
retmax: 10
ttl: 24
baseurl: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/
# queried database, e.g. "pubmed" or "pmc"; can be a vector
db: [pubmed, pmc]
term: bioconductor
# Sorting of query results. This one is database-specific; possible values include
# pubmed: pub+date, first+author, last+author, journal, title, relevance
# pmc: print+pub+date, electronic+pub+date, journal, pmc+live+date
# For default sorting leave this field out
sort: [ "", electronic+pub+date]
# CHANGE THIS when it becomes apparent which future versions of BioC will
# work with which versions of R:
r_ver_for_bioc_ver:
"1.6": "2.1"
"1.7": "2.2"
"1.8": "2.3"
"1.9": "2.4"
"2.0": "2.5"
"2.1": "2.6"
"2.2": "2.7"
"2.3": "2.8"
"2.4": "2.9"
"2.5": "2.10"
"2.6": "2.11"
"2.7": "2.12"
"2.8": "2.13"
"2.9": "2.14"
"2.10": "2.15"
"2.11": "2.15" # R switching to yearly releases, BioC remaining the same
"2.12": "3.0"
"2.13": "3.0"
"2.14": "3.1"
"3.0": "3.1"
"3.1": "3.2"
"3.2": "3.2"
"3.3": "3.3"
"3.4": "3.3"
"3.5": "3.4"
"3.6": "3.4"
"3.7": "3.5"
"3.8": "3.5"
"3.9": "3.6"
"3.10": "3.6"
"3.11": "4.0"
"3.12": "4.0"
"3.13": "4.1"
"3.14": "4.1"
"3.15": "4.2"
"3.16": "4.2"
"3.17": "4.3"
"3.18": "4.3"
"3.19": "4.4"
"3.20": "4.4"
"3.21": "4.5"
# UPDATE THIS when we release a version
release_dates: # old info from http://en.wikipedia.org/wiki/Bioconductor#Milestones
"1.0": "1/5/2001"
"1.1": "11/19/2002"
"1.2": "5/29/2003"
"1.3": "10/30/2003"
"1.4": "5/17/2004"
"1.5": "10/25/2004"
"1.6": "5/18/2005"
"1.7": "10/14/2005"
"1.8": "4/27/2006"
"1.9": "10/4/2006"
"2.0": "4/26/2007"
"2.1": "10/8/2007"
"2.2": "5/1/2008"
"2.3": "10/22/2008"
"2.4": "4/21/2009"
"2.5": "10/28/2009"
"2.6": "4/23/2010"
"2.7": "10/18/2010"
"2.8": "4/14/2011"
"2.9": "11/1/2011"
"2.10": "4/2/2012"
"2.11": "10/3/2012"
"2.12": "4/4/2013"
"2.13": "10/15/2013"
"2.14": "4/14/2014"
"3.0": "10/14/2014"
"3.1": "4/17/2015"
"3.2": "10/14/2015"
"3.3": "5/4/2016"
"3.4": "10/18/2016"
"3.5": "4/25/2017"
"3.6": "10/31/2017"
"3.7": "05/01/2018"
"3.8": "10/31/2018"
"3.9": "05/03/2019"
"3.10": "10/30/2019"
"3.11": "04/28/2020"
"3.12": "10/28/2020"
"3.13": "05/20/2021"
"3.14": "10/27/2021"
"3.15": "04/27/2022"
"3.16": "11/02/2022"
"3.17": "04/26/2023"
"3.18": "10/25/2023"
"3.19": "05/01/2024"
"3.20": "10/30/2024"
release_last_built_dates:
'2.0': 09/12/2007
'2.1': 04/09/2008
'2.2': 10/16/2008
'2.3': 04/18/2009
'2.4': 10/20/2009
'2.5': 04/03/2010
'2.6': 10/05/2010
'2.7': 04/07/2011
'2.8': 10/21/2011
'2.9': 03/24/2012
'2.10': 09/24/2012
'2.11': 03/25/2013
'2.12': 10/09/2013
'2.13': 04/05/2014
'2.14': 10/08/2014
'3.0': 04/10/2015
'3.1': 10/09/2015
'3.2': 04/23/2016
'3.3': 10/13/2016
'3.4': 04/15/2017
'3.5': 10/18/2017
'3.6': 04/12/2018
'3.7': 10/17/2018
'3.8': 04/16/2019
'3.9': 10/16/2019
'3.10': 04/15/2020
'3.11': 10/17/2020
'3.12': 05/06/2021
'3.13': 10/15/2021
'3.14': 04/13/2022
'3.15': 10/19/2022
'3.16': 04/12/2023
'3.17': 10/16/2023
'3.18': 04/17/2024
'3.19': 10/18/2024
mirrors:
- 0-Bioconductor:
- institution: Bioconductor, automatic redirection to servers worldwide
institution_url: https://bioconductor.org
contact: Bioconductor Maintainer
contact_email: [email protected]
city: World-wide
mirror_url: http://bioconductor.org/
https_mirror_url: https://bioconductor.org/
rsync: secure_mirror_from_master
country_code: us
- USA:
- institution: Posit Software, PBC
institution_url: https://posit.co/
contact: Joshua Spiewak
contact_email: [email protected]
city: Boston
mirror_url: http://bioconductor.posit.co/
https_mirror_url: https://bioconductor.posit.co/
rsync: secure_mirror_from_master
country_code: us
- Germany:
- institution: Department of Statistics, TU Dortmund
institution_url: https://www.statistik.tu-dortmund.de/
contact: Uwe Ligges
contact_email: [email protected]
mirror_url: http://bioconductor.statistik.tu-dortmund.de/
https_mirror_url: https://bioconductor.statistik.tu-dortmund.de/
rsync:
city: Dortmund
country_code: de
- institution: GWDG
institution_url: https://ftp.gwdg.de/
contact: Tim Ehlers and Steffen Klemer
contact_email: [email protected]
mirror_url: http://ftp.gwdg.de/pub/misc/bioconductor/
https_mirror_url: https://ftp.gwdg.de/pub/misc/bioconductor/
rsync: secure_mirror_from_master
city: Gottingen
country_code: de
- Japan:
- institution: RIKEN Advanced Center for Computing and Communication
institution_url: https://accc.riken.jp/en/
contact: Itoshi NIKAIDO, Ph.D.
contact_email: [email protected]
mirror_url: http://bioconductor.riken.jp/
https_mirror_url: https://bioconductor.riken.jp/
rsync: secure_mirror_from_master
country_code: jp
city: Wako
- Taiwan:
- institution: National Center for High-performance Computing
institution_url: https://www.nchc.org.tw/
contact: Chenkai Sun
contact_email: [email protected]
mirror_url: http://free.nchc.org.tw/bioconductor/
https_mirror_url: https://free.nchc.org.tw/bioconductor/
rsync: secure_mirror_from_master
country_code: tw
city: Hsinchu
- China:
- institution: TUNA Mirror Site, Tsinghua University
institution_url: mirrors.tuna.tsinghua.edu.cn
contact: Miao Wang
contact_email: [email protected]
mirror_url: http://mirrors.tuna.tsinghua.edu.cn/bioconductor/
https_mirror_url: https://mirrors.tuna.tsinghua.edu.cn/bioconductor/
rsync: secure_mirror_from_master
country_code: cn
city: Peking
- institution: eScience Center, Nanjing University
institution_url: https://sci.nju.edu.cn/
contact: Ge Yao
contact_email: [email protected]
mirror_url: http://mirrors.nju.edu.cn/bioconductor/
https_mirror_url: https://mirrors.nju.edu.cn/bioconductor/
rsync: secure_mirror_from_master
city: Nanjing
country_code: cn
- institution: University of Science and Technology of China (USTC)
institution_url: https://ustc.edu.cn
contact: Linux User Group (LUG) @ USTC
contact_email: [email protected]
mirror_url: http://mirrors.ustc.edu.cn/bioc/
https_mirror_url: https://mirrors.ustc.edu.cn/bioc/
rsync: secure_mirror_from_master
city: Hefei Anhui
country_code: cn
- institution: High-Performance Computing Center, Westlake University
institution_url: https://www.westlake.edu.cn/
contact: Ling Yang
contact_email: [email protected]
mirror_url: https://mirrors.westlake.edu.cn/bioconductor
https_mirror_url: https://mirrors.westlake.edu.cn/bioconductor
rsync: secure_mirror_from_master
city: Hangzhou Westlake
country_code: cn
- institution: Zhejiang University
institution_url: https://www.zju.edu.cn/
contact: ZJUSCT Team Falcon
contact_email: [email protected]
mirror_url: https://mirrors.zju.edu.cn/bioconductor
https_mirror_url: https://mirrors.zju.edu.cn/bioconductor
rsync: TUNA
city: Zhejiang University
country_code: cn
- Norway:
- institution: University of Bergen
institution_url: https://www.uib.no/
contact: Trond Davidsen
contact_email: [email protected]
mirror_url: http://bioconductor.uib.no/
https_mirror_url: https://bioconductor.uib.no/
rsync: secure_mirror_from_master
city: Bergen
country_code: "no"
- Italy:
- institution: University of Pisa
institution_url: https://www.unipi.it/
contact: Fabio Pratelli
contact_email: [email protected]
mirror_url: http://bioconductor.unipi.it
https_mirror_url: https://bioconductor.unipi.it
rsync: secure_mirror_from_master
city: Pisa
country_code: it
- Korea:
- institution: CRAN Asia
institution_url: https://cran.asia
contact: Seongho Bae
contact_email: [email protected]
mirror_url: http://cran.asia
https_mirror_url: https://cran.asia
rsync: secure_mirror_from_master
city: Seoul
country_code: kr
- Australia:
- institution: AARNet Pty Ltd
institution_url: https://aarnet.edu.au
contact: AARNet Operations Center
contact_email: [email protected]
mirror_url: http://mirror.aarnet.edu.au/pub/bioconductor
https_mirror_url: https://mirror.aarnet.edu.au/pub/bioconductor
rsync: secure_mirror_from_master
city: Sydney
country_code: au
- Denmark:
- institution: dotsrc
institution_url: https://dotsrc.org/
contact: Anders Trier Olesen
contact_email: [email protected]
mirror_url: http://mirrors.dotsrc.org/bioconductor/
https_mirror_url: https://mirrors.dotsrc.org/bioconductor/
rsync: secure_mirror_from_master
city: Aalborg
country_code: dk
- Sweden:
- institution: Academic Computer Club Umea
institution_url: https://www.accum.se/
contact: FTP admins
contact_email: [email protected]
mirror_url: http://mirror.accum.se/mirror/bioconductor.org/
https_mirror_url: https://mirror.accum.se/mirror/bioconductor.org/
rsync: secure_mirror_from_master
city: Umea
country_code: se