diff --git a/docker-files/docker-apollo-config.groovy b/docker-files/docker-apollo-config.groovy
index b5629225b..ac1770faf 100644
--- a/docker-files/docker-apollo-config.groovy
+++ b/docker-files/docker-apollo-config.groovy
@@ -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
@@ -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")?:"apollo@localhost.com"
+        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") ?: "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)
-        ]
-    ]
+  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
+       }
+   }
 }
+