forked from GMOD/Apollo
/
docker-apollo-config.groovy
194 lines (179 loc) · 8.3 KB
/
docker-apollo-config.groovy
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println "WEBAPOLLO environment"
System.getenv().each {
if (it.key.contains("APOLLO") || it.key.contains("CHADO")) {
println it.key + " " + it.value
}
}
Boolean checkBooleanEnvironment(String environment,Boolean defaultValue ){
if(System.getenv(environment)==null || System.getenv(environment).trim().replaceAll(/"/,"").replaceAll(/'/,"").size()==0){
println "'${environment}' not specified '${System.getenv(environment)}' so returning default '${defaultValue}'."
return defaultValue
}
boolean returnValue = Boolean.valueOf(System.getenv(environment))
println "Setting '${environment}' as '${System.getenv(environment)}' to '${returnValue}'."
return returnValue
}
environments {
development {
}
test {
}
production {
dataSource {
dbCreate = "update"
username = System.getenv("WEBAPOLLO_DB_USERNAME") ?: "apollo"
password = System.getenv("WEBAPOLLO_DB_PASSWORD") ?: "apollo"
driverClassName = "org.postgresql.Driver"
dialect = "org.hibernate.dialect.PostgresPlusDialect"
url = "jdbc:postgresql://${System.getenv("WEBAPOLLO_DB_HOST") ?: "127.0.0.1"}/${System.getenv("WEBAPOLLO_DB_NAME") ?: "apollo"}"
properties {
// See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = false
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
}
}
if (System.getenv("WEBAPOLLO_USE_CHADO") == "true") {
dataSource_chado {
dbCreate = "update"
username = System.getenv("CHADO_DB_USERNAME") ?: "apollo"
password = System.getenv("CHADO_DB_PASSWORD") ?: "apollo"
driverClassName = "org.postgresql.Driver"
dialect = "org.hibernate.dialect.PostgresPlusDialect"
url = "jdbc:postgresql://${System.getenv("CHADO_DB_HOST") ?: "127.0.0.1"}/${System.getenv("CHADO_DB_NAME") ?: "chado"}"
properties {
// See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = false
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
}
}
}
}
}
if (checkBooleanEnvironment("WEBAPOLLO_DEBUG",false)) {
log4j.main = {
debug "grails.app"
}
}
apollo {
common_data_directory = System.getenv("WEBAPOLLO_COMMON_DATA") ? System.getenv("WEBAPOLLO_COMMON_DATA") : "/data/temporary/apollo_data"
default_minimum_intron_size = System.getenv("WEBAPOLLO_MINIMUM_INTRON_SIZE") ? System.getenv("WEBAPOLLO_MINIMUM_INTRON_SIZE").toInteger() : 1
history_size = System.getenv("WEBAPOLLO_HISTORY_SIZE") ? System.getenv("WEBAPOLLO_HISTORY_SIZE").toInteger() : 0
overlapper_class = System.getenv("WEBAPOLLO_OVERLAPPER_CLASS") ?: "org.bbop.apollo.sequence.OrfOverlapper"
use_cds_for_new_transcripts = checkBooleanEnvironment("WEBAPOLLO_CDS_FOR_NEW_TRANSCRIPTS",false)
count_annotations = checkBooleanEnvironment("WEBAPOLLO_COUNT_ANNOTATIONS",true)
add_merged_commented = checkBooleanEnvironment("WEBAPOLLO_ADD_MERGED_COMMENT",true)
feature_has_dbxrefs = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_DBXREFS",true)
feature_has_attributes = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_ATTRS",true)
feature_has_pubmed_ids = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_PUBMED",true)
feature_has_go_ids =checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_GO",true)
calculate_non_canonical_splice_sites = checkBooleanEnvironment("WEBAPOLLO_CALCULATE_NON_CANONICAL_SPLICE_SITES",true)
feature_has_comments = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_COMMENTS",true)
feature_has_status = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_STATUS",true)
translation_table = "/config/translation_tables/ncbi_" + (System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ?: "1") + "_translation_table.txt"
get_translation_code = System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ? System.getenv("WEBAPOLLO_TRANSLATION_TABLE").toInteger() : 1
fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // automatically loaded // https://genome.ucsc.edu/goldenPath/help/blatSpec.html
make_blast_db_exe = "/usr/local/bin/makeblastdb"
// TODO: should come from config or via preferences database
splice_donor_sites = System.getenv("WEBAPOLLO_SPLICE_DONOR_SITES") ? System.getenv("WEBAPOLLO_SPLICE_DONOR_SITES").split(",") : ["GT"]
splice_acceptor_sites = System.getenv("WEBAPOLLO_SPLICE_ACCEPTOR_SITES") ? System.getenv("WEBAPOLLO_SPLICE_ACCEPTOR_SITES").split(",") : ["AG"]
gff3.source = System.getenv("WEBAPOLLO_GFF3_SOURCE") ?: "."
google_analytics = System.getenv("WEBAPOLLO_GOOGLE_ANALYTICS_ID") ?: ["UA-62921593-1"]
admin {
username = System.getenv("APOLLO_ADMIN_EMAIL") ?: "admin@local.host"
password = System.getenv("APOLLO_ADMIN_PASSWORD") ?: "password"
firstName = System.getenv("APOLLO_ADMIN_FIRST_NAME") ?: "Ad"
lastName = System.getenv("APOLLO_ADMIN_LAST_NAME") ?: "min"
}
authentications = [
[
"name":"Remote User Authenticator",
"className":"remoteUserAuthenticatorService",
"active": checkBooleanEnvironment("WEBAPOLLO_REMOTE_USER_AUTH",false)
],
[
"name":"Username Password Authenticator",
"className":"usernamePasswordAuthenticatorService",
"active": checkBooleanEnvironment("WEBAPOLLO_USER_PASSWORD_AUTH",true)
]
]
sequence_search_tools {
blast_nuc {
search_exe = "/usr/local/bin/blastn"
search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
name = "Blast nucleotide"
}
blast_prot {
search_exe = "/usr/local/bin/tblastn"
search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
name = "Blast protein to translated nucleotide"
}
}
}
jbrowse {
git {
url = "https://github.com/GMOD/jbrowse"
branch = "1.16.11-release"
}
plugins {
ScreenShotPlugin{
git = 'https://github.com/bhofmei/jbplugin-screenshot.git'
branch = 'master'
alwaysRecheck = "true"
alwaysPull = "true"
}
ColorByCDS{
git = 'https://github.com/scottcain/colorbycds.git'
branch = 'master'
alwaysRecheck = "true"
alwaysPull = "true"
}
MAFViewer{
git = 'https://github.com/cmdcolin/mafviewer.git'
branch = 'master'
alwaysRecheck = "true"
alwaysPull = "true"
}
FeatureSequence{
git = 'https://github.com/twsaari/FeatureSequence.git'
branch = 'master'
alwaysRecheck = "true"
alwaysPull = "true"
}
// WormbaseGlyphs{
// git = 'https://github.com/nathandunn/WormbaseGlyphs.git'
// branch = 'master'
// alwaysRecheck = "true"
// alwaysPull = "true"
// }
}
}