-
Notifications
You must be signed in to change notification settings - Fork 17
/
Copy pathamigo.yaml.tomodachi
217 lines (217 loc) · 10.3 KB
/
amigo.yaml.tomodachi
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
---
AMIGO_1X_PUBLIC_CGI_BASE_URL:
comment: The public URL of an available AmiGO 1.x instance for link references.
type: url
value: http://amigo1.geneontology.org/cgi-bin/amigo
AMIGO_API_PORT:
comment: OPTIONAL. The port on which to make available the experimental AmiGO JSON API. Defaults to 6455.
type: number
value: 6455
AMIGO_BALANCER:
comment: 'Mark this AmiGO 2 installation as behind a load balanacer or similar system. The practical effect of this flag is that if AmiGO detects *.error files (usually created by the global-message.pl script), it will return a 503 page signalling any upstream system that the instance is not currently ready.'
type: boolean
value: 1
AMIGO_BETA:
comment: Mark the AmiGO site as BETA (triggers some changes in variables and installed features).
type: boolean
value: 1
AMIGO_BROWSE_FILTER_IDSPACE:
comment: An optional field to filter restrict to globally restrict to a certain ontology during some browsing.
type: string
value: GO
AMIGO_DOWNLOAD_LIMIT:
comment: The download size that AmiGO will default to for the UI.
type: number
value: 100000
AMIGO_DYNAMIC_PATH:
comment: The full path to the location of the perl binaries.
type: directory
value: /home/bbop/local/src/git/amigo/perl/bin
AMIGO_DYNAMIC_URL:
comment: The URL that AMIGO_DYNAMIC_PATH maps to.
type: url
value: http://tomodachi.berkeleybop.org
AMIGO_FOR_GO:
comment: This flag indicates whether or not your AmiGO instance is for the GO, or a more generic instance. If you are trying to run AmiGO locally, probably "1"; if you are trying to have your own AmiGO with different ontologies, data, etc., probably 0.
type: boolean
value: 1
AMIGO_GOOGLE_ANALYTICS_ID:
comment: Google analytics ID. Optional.
type: string
value: 'UA-42073879-1'
AMIGO_LAYOUT_SEARCH:
comment: A whitespace separated list of class IDs to use for live search tabs on the search page.
type: list
value:
- annotation
- ontology
- bioentity
- model_annotation
- noctua_model_meta
- family
- general
- bbop_term_ac
AMIGO_PRIVATE_GOLR_URL:
comment: The (optional) private URL of the GOlr server (including slash); this is the one used for loading. Can be the same as the public URL if you have no proxy or firewall to deal with.
type: url
value: http://localhost:8080/solr/
AMIGO_PUBLIC_GALAXY_URL:
comment: Please enter the public URL of the Galaxy server.
type: url
value: http://galaxy.berkeleybop.org/
AMIGO_PUBLIC_GOLR_BULK_URL:
comment: The public URL of the GOlr bulk download server (including slash); possibly the same as AMIGO_PUBLIC_GOLR_URL.
type: url
value: http://amigo-dev-golr.berkeleybop.org/
AMIGO_PUBLIC_GOLR_URL:
comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
type: url
value: http://amigo-dev-golr.berkeleybop.org/
AMIGO_PUBLIC_NOCTUA_URL:
comment: The public URL of the Noctua system (including slash).
type: url
value: http://noctua.berkeleybop.org/
AMIGO_ROOT:
comment: 'Unless you are doing something strange, the parent directory of this file.'
type: directory
value: /home/bbop/local/src/git/amigo
AMIGO_ROOT_TERMS:
comment: 'For some widgets, we need to know what root terms you are going to be considering in your ontology. Requires both "id" and "label" to be defined.'
type: json
value:
- id: GO:0008150
label: biological process
- id: GO:0005575
label: cellular component
- id: GO:0003674
label: molecular function
AMIGO_SERVER_NAME:
comment: 'The name by which your AmiGO instance wishes to known--think load balancer or cache situations. If you would rather this information not be reported, leave blank.'
type: string
value: tomodachi
AMIGO_STATIC_PATH:
comment: The full path to a usable static document directory where static and staging are located.
type: directory
value: /home/bbop/local/src/git/amigo/static
AMIGO_STATIC_URL:
comment: The URL for the static content. Can be local or remote.
type: url
value: http://tomodachi.berkeleybop.org/static
AMIGO_TERM_REGEXP:
comment: The regular expressions to identify internal ontology ids.
type: string
value: 'all|GO:[0-9]{7}'
AMIGO_VERBOSE:
comment: Log verbose AmiGO debugging messages.
type: boolean
value: 0
AMIGO_WORKING_PATH:
comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
type: directory
value: /tmp
GO_API_URL:
comment: Base URL of the GO API
type: url
value: ''
GOLR_CATALOG_LOCATION:
comment: The location of the GO catalog file for various work.
type: file
value: '/home/bbop/local/src/svn/geneontology.org/trunk/ontology/extensions/catalog-v001.xml'
GOLR_GAF_LIST:
comment: The list of GAFs to load.
type: list
value:
- http://www.geneontology.org/gene-associations/submission/paint/pre-submission/gene_association.paint_other.gaf
- http://www.geneontology.org/gene-associations/gene_association.GeneDB_Lmajor.gz
- http://www.geneontology.org/gene-associations/gene_association.GeneDB_Pfalciparum.gz
- http://www.geneontology.org/gene-associations/gene_association.GeneDB_Tbrucei.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Atumefaciens.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Ddadantii.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Mgrisea.gz
- http://www.geneontology.org/gene-associations/gene_association.PAMGO_Oomycetes.gz
- http://www.geneontology.org/gene-associations/gene_association.aspgd.gz
- http://www.geneontology.org/gene-associations/gene_association.cgd.gz
- http://www.geneontology.org/gene-associations/gene_association.dictyBase.gz
- http://www.geneontology.org/gene-associations/gene_association.ecocyc.gz
- http://www.geneontology.org/gene-associations/gene_association.fb.gz
- http://www.geneontology.org/gene-associations/goa_chicken.gaf.gz
- http://www.geneontology.org/gene-associations/goa_chicken_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_chicken_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_cow.gaf.gz
- http://www.geneontology.org/gene-associations/goa_cow_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_cow_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_dog.gaf.gz
- http://www.geneontology.org/gene-associations/goa_dog_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_dog_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_human.gaf.gz
- http://www.geneontology.org/gene-associations/goa_human_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_human_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_pig.gaf.gz
- http://www.geneontology.org/gene-associations/goa_pig_complex.gaf.gz
- http://www.geneontology.org/gene-associations/goa_pig_rna.gaf.gz
- http://www.geneontology.org/gene-associations/goa_uniprot_all_noiea.gaf.gz
- http://www.geneontology.org/gene-associations/gene_association.gramene_oryza.gz
- http://www.geneontology.org/gene-associations/gene_association.jcvi.gz
- http://www.geneontology.org/gene-associations/gene_association.mgi.gz
- http://www.geneontology.org/gene-associations/gene_association.pombase.gz
- http://www.geneontology.org/gene-associations/gene_association.pseudocap.gz
- http://www.geneontology.org/gene-associations/gene_association.rgd.gz
- http://www.geneontology.org/gene-associations/gene_association.sgd.gz
- http://www.geneontology.org/gene-associations/gene_association.sgn.gz
- http://www.geneontology.org/gene-associations/gene_association.tair.gz
- http://www.geneontology.org/gene-associations/gene_association.wb.gz
- http://www.geneontology.org/gene-associations/gene_association.zfin.gz
GOLR_METADATA_LIST:
comment: 'The full path to the YAML config files directory. In that directory, all files like *config.yaml will be scanned for use.'
type: list
value:
- '~/local/src/git/amigo/metadata/ont-config.yaml'
- '~/local/src/git/amigo/metadata/bio-config.yaml'
- '~/local/src/git/amigo/metadata/bio-config.browse.yaml'
- '~/local/src/git/amigo/metadata/ann-config.yaml'
- '~/local/src/git/amigo/metadata/ann-config.browse.yaml'
- '~/local/src/git/amigo/metadata/general-config.yaml'
- '~/local/src/git/amigo/metadata/model-ann-config.yaml'
- '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
- '~/local/src/git/amigo/metadata/protein-family-config.yaml'
- '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
GOLR_METADATA_ONTOLOGY_LOCATION:
comment: The full path to the ontology YAML config file. This is core for any ontology-related load.
type: file
value: '/home/bbop/local/src/git/amigo/metadata/ont-config.yaml'
GOLR_NOCTUA_ENRICHED_MODEL_PATH:
comment: The list of ontologies to load.
type: directory
value: '/home/bbop/local/src/git/noctua-models/models/'
GOLR_ONTOLOGY_LIST:
comment: The list of ontologies to load.
type: list
value:
- http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl
- http://purl.obolibrary.org/obo/eco.owl
- http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
- http://purl.obolibrary.org/obo/cl/cl-basic.owl
- http://purl.obolibrary.org/obo/go/extensions/gorel.owl
- http://purl.obolibrary.org/obo/pato.owl
- http://purl.obolibrary.org/obo/po.owl
- http://purl.obolibrary.org/obo/chebi.owl
- http://purl.obolibrary.org/obo/uberon/basic.owl
- http://purl.obolibrary.org/obo/wbbt.owl
- http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl
- http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl
GOLR_PANTHER_FILE_PATH:
comment: The location of the cleaned PANTHER file for the proper loading into GOlr.
type: directory
value: '/home/bbop/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/'
OWLTOOLS_MAX_MEMORY:
comment: The maximum amount of memory to give OWLTools processes.
type: string
value: 192G
OWLTOOLS_USE_MERGE_IMPORT:
comment: Whether or not to include --merge-import http://purl.obolibrary.org/obo/go/extensions/go-gaf.owl.
type: boolean
value: 1
OWLTOOLS_USE_REMOVE_DISJOINTS:
comment: Whether or not to include --remove-disjoints.
type: boolean
value: 1