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Updated Apollo config file #4

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Updated Apollo config file #4

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f92d388
updated docker-apollo-config.groovy to get variables from the shell e…
VernonChapman-USDA Sep 18, 2022
4929d40
updated the default apollo config to get more values from the environ…
VernonChapman-USDA Sep 19, 2022
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242 changes: 100 additions & 142 deletions docker-files/docker-apollo-config.groovy
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Original file line number Diff line number Diff line change
@@ -1,38 +1,34 @@
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 {
}
// 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 = System.getenv("WEBAPOLLO_DB_USERNAME") ?: "apollo"
password = System.getenv("WEBAPOLLO_DB_PASSWORD") ?: "apollo"
driverClassName = System.getenv("WEBAPOLLO_DB_DRIVER") ?:"org.postgresql.Driver"
dialect = System.getenv("WEBAPOLLO_DB_DIALECT") ?: "org.hibernate.dialect.PostgresPlusDialect"
url = System.getenv("WEBAPOLLO_DB_URI") ?: "jdbc:postgresql://127.0.0.1/apollo"
}
}
production {
dataSource {
dbCreate = "update"
dataSource{
dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
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"}"
driverClassName = System.getenv("WEBAPOLLO_DB_DRIVER") ?:"org.postgresql.Driver"
dialect = System.getenv("WEBAPOLLO_DB_DIALECT") ?: "org.hibernate.dialect.PostgresPlusDialect"
url = System.getenv("WEBAPOLLO_DB_URI") ?: "jdbc:postgresql://127.0.0.1/apollo"

properties {
// See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
jmxEnabled = false
jmxEnabled = true
initialSize = 5
maxActive = 50
minIdle = 5
Expand All @@ -51,131 +47,93 @@ environments {
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"
}
}


// Uncomment to make changes
//
// not quite default apollo settings
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
admin{
username = System.getenv("APOLLO_ADMIN_EMAIL")?:"[email protected]"
password = System.getenv("APOLLO_ADMIN_PASSWORD")?:"apollo"
firstName = System.getenv("APOLLO_ADMIN_FIRST_NAME")?: "Apollo"
lastName = System.getenv("APOLLO_ADMIN_LAST_NAME")?: "User"
}
default_minimum_intron_size = 1
history_size = 0
overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"
track_name_comparator = "/config/track_name_comparator.js"
use_cds_for_new_transcripts = true
user_pure_memory_store = true
translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"
is_partial_translation_allowed = false // unused so far
get_translation_code = 1
only_owners_delete = false
google_analytics = ["UA-49907870-1","UA-62921593-1", "UA-27627304-1"]
sequence_search_tools = [
blat_nuc: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
name: "Blat nucleotide",
params: ""
],
blat_prot: [
search_exe: "/usr/local/bin/blat",
search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
name: "Blat protein",
params: ""
]
]

fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // automatically loaded // https://genome.ucsc.edu/goldenPath/help/blatSpec.html

// 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"]
splice_donor_sites = [ "GT" ]
splice_acceptor_sites = [ "AG"]
gff3.source= "Apollo"
bootstrap = false

admin {
username = System.getenv("APOLLO_ADMIN_EMAIL") ?: "[email protected]"
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)
]
]
info_editor = {
feature_types = "default"
attributes = true
dbxrefs = true
pubmed_ids = true
go_ids = true
comments = true
}
}

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"
git {
url= "https://github.com/GMOD/jbrowse"
tag = "1.16.11-release"
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 {
WebApollo{
included = true
}
NeatHTMLFeatures{
included = true
}
FeatureSequence{
git = 'https://github.com/twsaari/FeatureSequence.git'
branch = 'master'
alwaysRecheck = "true"
alwaysPull = "true"
NeatCanvasFeatures{
included = true
}
// WormbaseGlyphs{
// git = 'https://github.com/nathandunn/WormbaseGlyphs.git'
// branch = 'master'
// alwaysRecheck = "true"
// alwaysPull = "true"
// }
}
RegexSequenceSearch{
included = true
}
HideTrackLabels{
included = true
}
NAL_CSS {
git = "https://github.com/NAL-i5K/NAL_CSS"
branch = "supports_1.16.5-release"
alwaysPull = true
alwaysRecheck = true
}
}
}