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sample-postgres-apollo-config.groovy
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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
// }
// }
}
}
//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"
//// }
// }
//}