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sample-postgres-apollo-config.groovy
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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
// }
// }
}
}
// 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 = "maint/1.12.5-apollo"
// alwaysPull = true
// alwaysRecheck = true
//
// // Warning: We are still testing the performance of NeatFeatures plugins in combination with Apollo.
// // We advise caution if enabling these plugins with Apollo until this process is finalized.
// }
// 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"
// }
// }
//}