forked from GMOD/Apollo
-
Notifications
You must be signed in to change notification settings - Fork 2
/
sample-postgres-apollo-config.groovy
188 lines (185 loc) · 7.41 KB
/
sample-postgres-apollo-config.groovy
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
environments {
development {
// sample config to turn on debug logging in development e.g. for apollo run-local
log4j.main = {
debug "grails.app"
}
// sample config to edit apollo specific configs in development mode
apollo {
gff3.source = "testing"
}
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "<CHANGEME>"
password = "<CHANGEME>"
driverClassName = "org.postgresql.Driver"
dialect = org.hibernate.dialect.PostgresPlusDialect
url = "jdbc:postgresql://localhost/apollo"
}
// dataSource_chado{
// dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
// username = "<CHANGEME>"
// password = "<CHANGEME>"
// driverClassName = "org.postgresql.Driver"
// dialect = org.hibernate.dialect.PostgresPlusDialect
// url = "jdbc:postgresql://localhost/apollo-chado"
// }
}
test {
dataSource{
dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "<CHANGEME>"
password = "<CHANGEME>"
driverClassName = "org.postgresql.Driver"
// dialect = org.hibernate.dialect.PostgresPlusDialect
dialect = "org.bbop.apollo.ImprovedPostgresDialect"
url = "jdbc:postgresql://localhost/apollo-test"
}
// dataSource_chado{
// dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
// username = "<CHANGEME>"
// password = "<CHANGEME>"
// driverClassName = "org.postgresql.Driver"
//// dialect = org.hibernate.dialect.PostgresPlusDialect
// dialect = "org.bbop.apollo.ImprovedPostgresDialect"
// url = "jdbc:postgresql://localhost/apollo-test-chado"
// }
}
production {
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
username = "<CHANGEME>"
password = "<CHANGEME>"
driverClassName = "org.postgresql.Driver"
dialect = org.hibernate.dialect.PostgresPlusDialect
url = "jdbc:postgresql://localhost/apollo-production"
properties {
// See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = true
initialSize = 5
maxActive = 50
minIdle = 5
maxIdle = 25
maxWait = 10000
maxAge = 10 * 60000
timeBetweenEvictionRunsMillis = 5000
minEvictableIdleTimeMillis = 60000
validationQuery = "SELECT 1"
validationQueryTimeout = 3
validationInterval = 15000
testOnBorrow = true
testWhileIdle = true
testOnReturn = false
jdbcInterceptors = "ConnectionState"
defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED
}
}
// dataSource_chado{
// dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
// username = "<CHANGEME>"
// password = "<CHANGEME>"
// driverClassName = "org.postgresql.Driver"
// dialect = org.hibernate.dialect.PostgresPlusDialect
// url = "jdbc:postgresql://localhost/apollo-production-chado"
// properties {
// // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
// jmxEnabled = true
// initialSize = 5
// maxActive = 50
// minIdle = 5
// maxIdle = 25
// maxWait = 10000
// maxAge = 10 * 60000
// timeBetweenEvictionRunsMillis = 5000
// minEvictableIdleTimeMillis = 60000
// validationQuery = "SELECT 1"
// validationQueryTimeout = 3
// validationInterval = 15000
// testOnBorrow = true
// testWhileIdle = true
// testOnReturn = false
// jdbcInterceptors = "ConnectionState"
// defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED
// }
// }
}
}
//apollo {
// gff3.source = "MyOrg" // also for GPAD export
// only_owners_delete = true
// common_data_directory = "/opt/temporary/apollo"
// calculate_non_canonical_splice_sites = false
// add_merged_comment = true
// count_annotations = false
// store_orig_id = false
// fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // get from // https://genome.ucsc.edu/goldenPath/help/blatSpec.html
// sequence_search_tools {
// blat_nuc {
// search_exe = "/usr/local/bin/blastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast nucleotide"
// params = ""
// }
// blat_prot {
// search_exe = "/usr/local/bin/tblastn"
// search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
// name = "Blast protein to translated nucleotide"
// params = ""
// //tmp_dir: "/opt/apollo/tmp" optional param
// }
// }
// extraTabs = [
// ['title': 'extra1', 'url': 'http://localhost:8080/apollo/annotator/report/'],
// ['title': 'extra2', 'content': '<b>Apollo</b> documentation <a href="https://genomearchitect.readthedocs.io/" target="_blank">linked here</a>']
// ['title': 'GGA', 'url': 'https://gitter.im/galaxy-genome-annotation/Lobby/~embed']
// ['title': 'JBrowse', 'url': 'https://gitter.im/GMOD/jbrowse/~embed']
// ]
//
//}
// Uncomment to change the default memory configurations
//grails.project.fork = [
// test : false,
// // configure settings for the run-app JVM
// run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the run-war JVM
// war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false],
// // configure settings for the Console UI JVM
// console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024]
//]
// Uncomment to make changes
//
//jbrowse {
// git {
// url= "https://github.com/GMOD/jbrowse"
// tag = "1.16.11-release"
//// branch = "dev"
//// hash = "09b71099bf73c50d37a0e911baf06b4975e3f6ca"
// alwaysPull = true
// alwaysRecheck = true
// }
// plugins {
// NeatHTMLFeatures{
// included = true
// }
// NeatCanvasFeatures{
// included = true
// }
// RegexSequenceSearch{
// included = true
// }
// HideTrackLabels{
// included = true
// }
//// MyVariantInfo {
//// git = 'https://github.com/GMOD/myvariantviewer'
//// branch = 'master'
//// alwaysRecheck = "true"
//// alwaysPull = "true"
//// }
//// SashimiPlot {
//// git = 'https://github.com/cmdcolin/sashimiplot'
//// branch = 'master'
//// alwaysPull = "true"
//// }
// }
//}