Container configuration
The services that constitutes Bonsai requires probably need to be configured to function properly or to enable/ disable some features. Docker containers are configured using parameters passed at runtime (such as those above). These parameters are separated by a colon and indicate <external>:<internal> respectively. For example, -p 8080:80 would expose port 80 from inside the container to be accessible from the host’s IP on port 8080 outside the container.
Ports
Parameter |
Function |
|---|---|
8000 |
WebUI |
8001 |
API |
27017 |
Mongo db |
6380 |
Redis |
Environmental variables
Frontend
Env |
Function |
Default |
|---|---|---|
API_INTERNAL_URL |
Container-container URL to API |
|
API_EXTERNAL_URL |
From browser URL to API |
|
TZ |
Timezone |
Etc/UTC |
- pydantic settings bonsai_app.config.Settings
Bonsai frontend configuration.
Show JSON schema
{ "title": "Settings", "description": "Bonsai frontend configuration.", "type": "object", "properties": { "api_internal_url": { "default": "http://api:8000", "description": "Internal container-container URL to the Bonsai API.", "title": "Api Internal Url", "type": "string" }, "api_external_url": { "default": "http://localhost:8001", "description": "External URL to the Bonsai API.", "title": "Api External Url", "type": "string" }, "timezone": { "default": "Etc/UTC", "enum": [ "Africa/Abidjan", "Africa/Accra", "Africa/Addis_Ababa", "Africa/Algiers", "Africa/Asmara", "Africa/Asmera", "Africa/Bamako", "Africa/Bangui", "Africa/Banjul", "Africa/Bissau", "Africa/Blantyre", "Africa/Brazzaville", "Africa/Bujumbura", "Africa/Cairo", "Africa/Casablanca", "Africa/Ceuta", "Africa/Conakry", "Africa/Dakar", "Africa/Dar_es_Salaam", "Africa/Djibouti", "Africa/Douala", "Africa/El_Aaiun", "Africa/Freetown", "Africa/Gaborone", "Africa/Harare", "Africa/Johannesburg", "Africa/Juba", "Africa/Kampala", "Africa/Khartoum", "Africa/Kigali", "Africa/Kinshasa", "Africa/Lagos", "Africa/Libreville", "Africa/Lome", "Africa/Luanda", "Africa/Lubumbashi", "Africa/Lusaka", "Africa/Malabo", "Africa/Maputo", "Africa/Maseru", "Africa/Mbabane", "Africa/Mogadishu", "Africa/Monrovia", "Africa/Nairobi", "Africa/Ndjamena", "Africa/Niamey", "Africa/Nouakchott", "Africa/Ouagadougou", "Africa/Porto-Novo", "Africa/Sao_Tome", "Africa/Timbuktu", "Africa/Tripoli", "Africa/Tunis", "Africa/Windhoek", "America/Adak", "America/Anchorage", "America/Anguilla", "America/Antigua", "America/Araguaina", "America/Argentina/Buenos_Aires", "America/Argentina/Catamarca", "America/Argentina/ComodRivadavia", "America/Argentina/Cordoba", "America/Argentina/Jujuy", "America/Argentina/La_Rioja", "America/Argentina/Mendoza", "America/Argentina/Rio_Gallegos", "America/Argentina/Salta", "America/Argentina/San_Juan", "America/Argentina/San_Luis", "America/Argentina/Tucuman", "America/Argentina/Ushuaia", "America/Aruba", "America/Asuncion", "America/Atikokan", "America/Atka", "America/Bahia", "America/Bahia_Banderas", "America/Barbados", "America/Belem", "America/Belize", "America/Blanc-Sablon", "America/Boa_Vista", "America/Bogota", "America/Boise", "America/Buenos_Aires", "America/Cambridge_Bay", "America/Campo_Grande", "America/Cancun", "America/Caracas", "America/Catamarca", "America/Cayenne", "America/Cayman", "America/Chicago", "America/Chihuahua", "America/Ciudad_Juarez", "America/Coral_Harbour", "America/Cordoba", "America/Costa_Rica", "America/Coyhaique", "America/Creston", "America/Cuiaba", "America/Curacao", "America/Danmarkshavn", "America/Dawson", "America/Dawson_Creek", "America/Denver", "America/Detroit", "America/Dominica", "America/Edmonton", "America/Eirunepe", "America/El_Salvador", "America/Ensenada", "America/Fort_Nelson", "America/Fort_Wayne", "America/Fortaleza", "America/Glace_Bay", "America/Godthab", "America/Goose_Bay", "America/Grand_Turk", "America/Grenada", "America/Guadeloupe", "America/Guatemala", "America/Guayaquil", "America/Guyana", "America/Halifax", "America/Havana", "America/Hermosillo", "America/Indiana/Indianapolis", "America/Indiana/Knox", "America/Indiana/Marengo", "America/Indiana/Petersburg", "America/Indiana/Tell_City", "America/Indiana/Vevay", "America/Indiana/Vincennes", "America/Indiana/Winamac", "America/Indianapolis", "America/Inuvik", "America/Iqaluit", "America/Jamaica", "America/Jujuy", "America/Juneau", "America/Kentucky/Louisville", "America/Kentucky/Monticello", "America/Knox_IN", "America/Kralendijk", "America/La_Paz", "America/Lima", "America/Los_Angeles", "America/Louisville", "America/Lower_Princes", "America/Maceio", "America/Managua", "America/Manaus", "America/Marigot", "America/Martinique", "America/Matamoros", "America/Mazatlan", "America/Mendoza", "America/Menominee", "America/Merida", "America/Metlakatla", "America/Mexico_City", "America/Miquelon", "America/Moncton", "America/Monterrey", "America/Montevideo", "America/Montreal", "America/Montserrat", "America/Nassau", "America/New_York", "America/Nipigon", "America/Nome", "America/Noronha", "America/North_Dakota/Beulah", "America/North_Dakota/Center", "America/North_Dakota/New_Salem", "America/Nuuk", "America/Ojinaga", "America/Panama", "America/Pangnirtung", "America/Paramaribo", "America/Phoenix", "America/Port-au-Prince", "America/Port_of_Spain", "America/Porto_Acre", "America/Porto_Velho", "America/Puerto_Rico", "America/Punta_Arenas", "America/Rainy_River", "America/Rankin_Inlet", "America/Recife", "America/Regina", "America/Resolute", "America/Rio_Branco", "America/Rosario", "America/Santa_Isabel", "America/Santarem", "America/Santiago", "America/Santo_Domingo", "America/Sao_Paulo", "America/Scoresbysund", "America/Shiprock", "America/Sitka", "America/St_Barthelemy", "America/St_Johns", "America/St_Kitts", "America/St_Lucia", "America/St_Thomas", "America/St_Vincent", "America/Swift_Current", "America/Tegucigalpa", "America/Thule", "America/Thunder_Bay", "America/Tijuana", "America/Toronto", "America/Tortola", "America/Vancouver", "America/Virgin", "America/Whitehorse", "America/Winnipeg", "America/Yakutat", "America/Yellowknife", "Antarctica/Casey", "Antarctica/Davis", "Antarctica/DumontDUrville", "Antarctica/Macquarie", "Antarctica/Mawson", "Antarctica/McMurdo", "Antarctica/Palmer", "Antarctica/Rothera", "Antarctica/South_Pole", "Antarctica/Syowa", "Antarctica/Troll", "Antarctica/Vostok", "Arctic/Longyearbyen", "Asia/Aden", "Asia/Almaty", "Asia/Amman", "Asia/Anadyr", "Asia/Aqtau", "Asia/Aqtobe", "Asia/Ashgabat", "Asia/Ashkhabad", "Asia/Atyrau", "Asia/Baghdad", "Asia/Bahrain", "Asia/Baku", "Asia/Bangkok", "Asia/Barnaul", "Asia/Beirut", "Asia/Bishkek", "Asia/Brunei", "Asia/Calcutta", "Asia/Chita", "Asia/Choibalsan", "Asia/Chongqing", "Asia/Chungking", "Asia/Colombo", "Asia/Dacca", "Asia/Damascus", "Asia/Dhaka", "Asia/Dili", "Asia/Dubai", "Asia/Dushanbe", "Asia/Famagusta", "Asia/Gaza", "Asia/Harbin", "Asia/Hebron", "Asia/Ho_Chi_Minh", "Asia/Hong_Kong", "Asia/Hovd", "Asia/Irkutsk", "Asia/Istanbul", "Asia/Jakarta", "Asia/Jayapura", "Asia/Jerusalem", "Asia/Kabul", "Asia/Kamchatka", "Asia/Karachi", "Asia/Kashgar", "Asia/Kathmandu", "Asia/Katmandu", "Asia/Khandyga", "Asia/Kolkata", "Asia/Krasnoyarsk", "Asia/Kuala_Lumpur", "Asia/Kuching", "Asia/Kuwait", "Asia/Macao", "Asia/Macau", "Asia/Magadan", "Asia/Makassar", "Asia/Manila", "Asia/Muscat", "Asia/Nicosia", "Asia/Novokuznetsk", "Asia/Novosibirsk", "Asia/Omsk", "Asia/Oral", "Asia/Phnom_Penh", "Asia/Pontianak", "Asia/Pyongyang", "Asia/Qatar", "Asia/Qostanay", "Asia/Qyzylorda", "Asia/Rangoon", "Asia/Riyadh", "Asia/Saigon", "Asia/Sakhalin", "Asia/Samarkand", "Asia/Seoul", "Asia/Shanghai", "Asia/Singapore", "Asia/Srednekolymsk", "Asia/Taipei", "Asia/Tashkent", "Asia/Tbilisi", "Asia/Tehran", "Asia/Tel_Aviv", "Asia/Thimbu", "Asia/Thimphu", "Asia/Tokyo", "Asia/Tomsk", "Asia/Ujung_Pandang", "Asia/Ulaanbaatar", "Asia/Ulan_Bator", "Asia/Urumqi", "Asia/Ust-Nera", "Asia/Vientiane", "Asia/Vladivostok", "Asia/Yakutsk", "Asia/Yangon", "Asia/Yekaterinburg", "Asia/Yerevan", "Atlantic/Azores", "Atlantic/Bermuda", "Atlantic/Canary", "Atlantic/Cape_Verde", "Atlantic/Faeroe", "Atlantic/Faroe", "Atlantic/Jan_Mayen", "Atlantic/Madeira", "Atlantic/Reykjavik", "Atlantic/South_Georgia", "Atlantic/St_Helena", "Atlantic/Stanley", "Australia/ACT", "Australia/Adelaide", "Australia/Brisbane", "Australia/Broken_Hill", "Australia/Canberra", "Australia/Currie", "Australia/Darwin", "Australia/Eucla", "Australia/Hobart", "Australia/LHI", "Australia/Lindeman", "Australia/Lord_Howe", "Australia/Melbourne", "Australia/NSW", "Australia/North", "Australia/Perth", "Australia/Queensland", "Australia/South", "Australia/Sydney", "Australia/Tasmania", "Australia/Victoria", "Australia/West", "Australia/Yancowinna", "Brazil/Acre", "Brazil/DeNoronha", "Brazil/East", "Brazil/West", "CET", "CST6CDT", "Canada/Atlantic", "Canada/Central", "Canada/Eastern", "Canada/Mountain", "Canada/Newfoundland", "Canada/Pacific", "Canada/Saskatchewan", "Canada/Yukon", "Chile/Continental", "Chile/EasterIsland", "Cuba", "EET", "EST", "EST5EDT", "Egypt", "Eire", "Etc/GMT", "Etc/GMT+0", "Etc/GMT+1", "Etc/GMT+10", "Etc/GMT+11", "Etc/GMT+12", "Etc/GMT+2", "Etc/GMT+3", "Etc/GMT+4", "Etc/GMT+5", "Etc/GMT+6", "Etc/GMT+7", "Etc/GMT+8", "Etc/GMT+9", "Etc/GMT-0", "Etc/GMT-1", "Etc/GMT-10", "Etc/GMT-11", "Etc/GMT-12", "Etc/GMT-13", "Etc/GMT-14", "Etc/GMT-2", "Etc/GMT-3", "Etc/GMT-4", "Etc/GMT-5", "Etc/GMT-6", "Etc/GMT-7", "Etc/GMT-8", "Etc/GMT-9", "Etc/GMT0", "Etc/Greenwich", "Etc/UCT", "Etc/UTC", "Etc/Universal", "Etc/Zulu", "Europe/Amsterdam", "Europe/Andorra", "Europe/Astrakhan", "Europe/Athens", "Europe/Belfast", "Europe/Belgrade", "Europe/Berlin", "Europe/Bratislava", "Europe/Brussels", "Europe/Bucharest", "Europe/Budapest", "Europe/Busingen", "Europe/Chisinau", "Europe/Copenhagen", "Europe/Dublin", "Europe/Gibraltar", "Europe/Guernsey", "Europe/Helsinki", "Europe/Isle_of_Man", "Europe/Istanbul", "Europe/Jersey", "Europe/Kaliningrad", "Europe/Kiev", "Europe/Kirov", "Europe/Kyiv", "Europe/Lisbon", "Europe/Ljubljana", "Europe/London", "Europe/Luxembourg", "Europe/Madrid", "Europe/Malta", "Europe/Mariehamn", "Europe/Minsk", "Europe/Monaco", "Europe/Moscow", "Europe/Nicosia", "Europe/Oslo", "Europe/Paris", "Europe/Podgorica", "Europe/Prague", "Europe/Riga", "Europe/Rome", "Europe/Samara", "Europe/San_Marino", "Europe/Sarajevo", "Europe/Saratov", "Europe/Simferopol", "Europe/Skopje", "Europe/Sofia", "Europe/Stockholm", "Europe/Tallinn", "Europe/Tirane", "Europe/Tiraspol", "Europe/Ulyanovsk", "Europe/Uzhgorod", "Europe/Vaduz", "Europe/Vatican", "Europe/Vienna", "Europe/Vilnius", "Europe/Volgograd", "Europe/Warsaw", "Europe/Zagreb", "Europe/Zaporozhye", "Europe/Zurich", "Factory", "GB", "GB-Eire", "GMT", "GMT+0", "GMT-0", "GMT0", "Greenwich", "HST", "Hongkong", "Iceland", "Indian/Antananarivo", "Indian/Chagos", "Indian/Christmas", "Indian/Cocos", "Indian/Comoro", "Indian/Kerguelen", "Indian/Mahe", "Indian/Maldives", "Indian/Mauritius", "Indian/Mayotte", "Indian/Reunion", "Iran", "Israel", "Jamaica", "Japan", "Kwajalein", "Libya", "MET", "MST", "MST7MDT", "Mexico/BajaNorte", "Mexico/BajaSur", "Mexico/General", "NZ", "NZ-CHAT", "Navajo", "PRC", "PST8PDT", "Pacific/Apia", "Pacific/Auckland", "Pacific/Bougainville", "Pacific/Chatham", "Pacific/Chuuk", "Pacific/Easter", "Pacific/Efate", "Pacific/Enderbury", "Pacific/Fakaofo", "Pacific/Fiji", "Pacific/Funafuti", "Pacific/Galapagos", "Pacific/Gambier", "Pacific/Guadalcanal", "Pacific/Guam", "Pacific/Honolulu", "Pacific/Johnston", "Pacific/Kanton", "Pacific/Kiritimati", "Pacific/Kosrae", "Pacific/Kwajalein", "Pacific/Majuro", "Pacific/Marquesas", "Pacific/Midway", "Pacific/Nauru", "Pacific/Niue", "Pacific/Norfolk", "Pacific/Noumea", "Pacific/Pago_Pago", "Pacific/Palau", "Pacific/Pitcairn", "Pacific/Pohnpei", "Pacific/Ponape", "Pacific/Port_Moresby", "Pacific/Rarotonga", "Pacific/Saipan", "Pacific/Samoa", "Pacific/Tahiti", "Pacific/Tarawa", "Pacific/Tongatapu", "Pacific/Truk", "Pacific/Wake", "Pacific/Wallis", "Pacific/Yap", "Poland", "Portugal", "ROC", "ROK", "Singapore", "Turkey", "UCT", "US/Alaska", "US/Aleutian", "US/Arizona", "US/Central", "US/East-Indiana", "US/Eastern", "US/Hawaii", "US/Indiana-Starke", "US/Michigan", "US/Mountain", "US/Pacific", "US/Samoa", "UTC", "Universal", "W-SU", "WET", "Zulu", "localtime" ], "minLength": 1, "title": "Timezone", "type": "string" }, "verify_ssl": { "anyOf": [ { "type": "boolean" }, { "format": "path", "type": "string" } ], "default": true, "description": "If SSL should be verifed for HTTPS requests to the API. Can also provide a path to the CA bundle that should be used.", "title": "Verify Ssl" }, "request_timeout": { "default": 60, "description": "Timeout for requests to API in seconds.", "title": "Request Timeout", "type": "integer" }, "secret_key": { "default": "not-so-secret", "description": "Secret key for encrypting session.", "format": "binary", "title": "Secret Key", "type": "string" }, "sample_view_similarity_limit": { "default": 10, "description": "Limit number of samples in sample view dendrogram.", "title": "Sample View Similarity Limit", "type": "integer" }, "sample_view_similarity_threshold": { "default": 0.9, "description": "Minimum similarity score for samples in the samples view dendrogram.", "title": "Sample View Similarity Threshold", "type": "number" }, "sample_view_typing_method": { "$ref": "#/$defs/TypingMethod", "default": "minhash", "description": "Typing method used for clustering samples in sample view dendrogram." }, "sample_view_cluster_method": { "$ref": "#/$defs/ClusterMethod", "default": "single", "description": "Clustering method used for dendrogram in sample view." }, "testing": { "default": false, "description": "Enable test mode to facilitate easier testing and development.", "title": "Testing", "type": "boolean" } }, "$defs": { "ClusterMethod": { "description": "Index of methods for hierarchical clustering of samples.", "enum": [ "single", "complete", "average", "neighbor_joining" ], "title": "ClusterMethod", "type": "string" }, "TypingMethod": { "description": "Supported typing methods.", "enum": [ "mlst", "cgmlst", "minhash" ], "title": "TypingMethod", "type": "string" } }, "additionalProperties": false }
- Config:
use_enum_values: bool = True
- Fields:
- field api_internal_url: str = 'http://api:8000'
Internal container-container URL to the Bonsai API.
- field sample_view_cluster_method: ClusterMethod = ClusterMethod.SINGLE
Clustering method used for dendrogram in sample view.
- field sample_view_similarity_threshold: float = 0.9
Minimum similarity score for samples in the samples view dendrogram.
- field sample_view_typing_method: TypingMethod = TypingMethod.MINHASH
Typing method used for clustering samples in sample view dendrogram.
- field tz: TimeZoneName = 'Etc/UTC' (alias 'timezone')
API service
Here are the general configuration options for the API service. See the documentation on login systems for information on how to configure LDAP based authentication.
Env |
Function |
Default |
|---|---|---|
ALLOWED_ORIGINS |
Configure allowed origins as commma separated list. |
|
DATABASE_NAME |
Database name |
bonsai |
DB_HOST |
Hostname of mongodb |
mongodb |
DB_PORT |
Mongodb port |
27017 |
REDIS_HOST |
Hostname of redis server |
redis |
REDIS_PORT |
Port of redis server |
6379 |
REFERENCE_GENOMES_DIR |
Path to directory with reference genomes |
/tmp/reference_genomes |
ANNOTATIONS_DIR |
Path to directory where genome annotation is stored |
/tmp/annotations |
SECRET_KEY |
Authentication token secret key |
|
ACCESS_TOKEN_EXPIRE_MINUTES |
Authentication token expiration time. |
180 |
- pydantic settings bonsai_api.config.Settings
API configuration.
Show JSON schema
{ "title": "Settings", "description": "API configuration.", "type": "object", "properties": { "allowed_origins": { "default": [], "items": { "type": "string" }, "title": "Allowed Origins", "type": "array" }, "database_name": { "default": "bonsai", "title": "Database Name", "type": "string" }, "db_host": { "default": "mongodb", "title": "Db Host", "type": "string" }, "db_port": { "default": "27017", "title": "Db Port", "type": "string" }, "max_connections": { "default": 10, "title": "Max Connections", "type": "integer" }, "min_connections": { "default": 10, "title": "Min Connections", "type": "integer" }, "redis_host": { "default": "redis", "title": "Redis Host", "type": "string" }, "redis_port": { "default": "6379", "title": "Redis Port", "type": "string" }, "reference_genomes_dir": { "default": "/tmp/reference_genomes", "title": "Reference Genomes Dir", "type": "string" }, "annotations_dir": { "default": "/tmp/annotations", "title": "Annotations Dir", "type": "string" }, "secret_key": { "default": "not-so-secret", "title": "Secret Key", "type": "string" }, "access_token_expire_minutes": { "default": 180, "title": "Access Token Expire Minutes", "type": "integer" }, "api_authentication": { "default": true, "title": "Api Authentication", "type": "boolean" }, "smtp": { "anyOf": [ { "$ref": "#/$defs/SmtpConfig" }, { "type": "null" } ], "default": null }, "email": { "$ref": "#/$defs/EmailConfig", "default": { "subject_prefix": "[ Bonsai ]", "sender": "do-not-reply@bonsai.app", "sender_name": "Bonsai" } }, "ldap_search_attr": { "default": "mail", "title": "Ldap Search Attr", "type": "string" }, "ldap_search_filter": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Search Filter" }, "ldap_base_dn": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Base Dn" }, "ldap_host": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Host" }, "ldap_port": { "default": 1389, "title": "Ldap Port", "type": "integer" }, "ldap_bind_dn": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Bind Dn" }, "ldap_secret": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Secret" }, "ldap_connection_timeout": { "default": 10, "title": "Ldap Connection Timeout", "type": "integer" }, "ldap_read_only": { "default": false, "title": "Ldap Read Only", "type": "boolean" }, "ldap_valid_names": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Valid Names" }, "ldap_private_key_password": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Private Key Password" }, "ldap_raise_exceptions": { "default": false, "title": "Ldap Raise Exceptions", "type": "boolean" }, "ldap_user_login_attr": { "default": "mail", "title": "Ldap User Login Attr", "type": "string" }, "force_attribute_value_as_list": { "default": false, "title": "Force Attribute Value As List", "type": "boolean" }, "ldap_use_ssl": { "default": false, "title": "Ldap Use Ssl", "type": "boolean" }, "ldap_use_tls": { "default": true, "title": "Ldap Use Tls", "type": "boolean" }, "ldap_tls_version": { "default": 3, "title": "Ldap Tls Version", "type": "integer" }, "ldap_require_cert": { "default": 2, "title": "Ldap Require Cert", "type": "integer" }, "ldap_client_private_key": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Client Private Key" }, "ldap_client_cert": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Client Cert" }, "ldap_ca_certs_file": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Ca Certs File" }, "ldap_ca_certs_path": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": "/usr/lib/ssl/certs", "title": "Ldap Ca Certs Path" }, "ldap_ca_certs_data": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Ldap Ca Certs Data" }, "lims_export_config": { "anyOf": [ { "format": "file-path", "type": "string" }, { "type": "null" } ], "default": null, "description": "Path to custom LIMS exporter YAML configuration.If omitted, the application will fall back the packaged default.", "examples": [ "/etc/bonsai/lims.yaml" ], "title": "Lims Export Config" } }, "$defs": { "EmailConfig": { "additionalProperties": false, "properties": { "subject_prefix": { "default": "[ Bonsai ]", "title": "Subject Prefix", "type": "string" }, "sender": { "default": "do-not-reply@bonsai.app", "title": "Sender", "type": "string" }, "sender_name": { "default": "Bonsai", "title": "Sender Name", "type": "string" } }, "title": "EmailConfig", "type": "object" }, "SmtpConfig": { "additionalProperties": false, "description": "SMTP server configuration.", "properties": { "host": { "title": "Host", "type": "string" }, "port": { "default": 25, "title": "Port", "type": "integer" }, "timeout": { "default": 60, "description": "Conection timeout in seconds.", "title": "Timeout", "type": "integer" }, "use_tls": { "default": false, "title": "Use Tls", "type": "boolean" }, "use_ssl": { "default": false, "title": "Use Ssl", "type": "boolean" } }, "required": [ "host" ], "title": "SmtpConfig", "type": "object" } }, "additionalProperties": false }
- Config:
env_file_encoding: str = utf-8
env_nested_delimiter: str = __
- Fields:
- field email: EmailConfig = EmailConfig(subject_prefix='[ Bonsai ]', sender='do-not-reply@bonsai.app', sender_name='Bonsai')
Minhash service
Env |
Function |
Default |
|---|---|---|
SIGNATURE_KMER_SIZE |
Kmer size used to build signature files. |
31 |
GENOME_SIGNATURE_DIR |
Path to directory where signatures are kept. |
/data/signature_db |
REDIS_HOST |
Redis server hostname |
redis |
REDIS_PORT |
Redis server port |
6379 |
Allele clustering service
Env |
Function |
Default |
|---|---|---|
REDIS_HOST |
Redis server hostname |
redis |
REDIS_PORT |
Redis server port |
6379 |
Volume mappings
Mouting directories and files from the host file system to the container is used to make assetes, such as reference genomes or configurations, available to the software. It can also be used to make data persistant accros updates to the container which is usefull for databases.
Please ensure that the mounted asset directory match the path specified in the service configuration.
Note
Please ensure that the container have permission to read mounted files and directories.
API service volumes
The API can serve reference genome sequences and annotation files to the integrated IGV browser. These could be stored on the host file system and mounted to the docker container.
Volume |
Function |
|---|---|
/tmp/reference_genomes |
Reference genomes for IGV. |
/tmp/annotations |
IGV annotation files. |
Minhash service volumes
The genome signatures sent to the minhash service container and written to disk. The directory should be mounted to the host file system for the data to be persistant. For more information see data persistance.
Volume |
Function |
|---|---|
/data/signature_db |
Directory for genome signatures. |