Helm chart config

The configuration for the Helm chart is provided as a YAML file. It has the following fields:

General Settings

Field	Type	Default	Description
`name`	String	”Loculus”	The name of the Loculus instance
`logo`	Object		Configuration for the logo
`logo.url`	String	Loculus logo	URL path to the logo image file
`logo.width`	Integer	100	Width of the logo in pixels
`logo.height`	Integer	100	Height of the logo in pixels
`accessionPrefix`	String	”LOC_“	Prefix used for accession numbers
`environment`	String	”server”	Deployment environment. Options: “local” for development, “server” for production.
`host`	String		Hostname where Loculus will be accessible. Used for generating URLs and configuring ingress.
`bannerMessage`	String	”This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.”	Banner message (as HTML) to display at the very top of the page
`welcomeMessageHTML`	String		A custom welcome message to be shown on the landing page
`additionalHeadHTML`	String		Additional HTML to inject into the `<head>` of pages
`createTestAccounts`	Boolean		If true, creates the users testuser and superuser (the username and password are the same).
`robotsNoindexHeader`	Boolean		If true, adds a noindex header to prevent search engine indexing
`seqSets.enabled`	Boolean		Enable/disable SeqSets. If false, `seqSets.crossRef` can be omitted.
`seqSets.crossRef`	Object		Configuration for CrossRef integration. Set to `null` to disable CrossRef integration (you can still use SeqSets without CrossRef DOIs).
`seqSets.crossRef.DOIPrefix`	String		The DOI prefix for SeqSets
`seqSets.crossRef.endpoint`	String		The API endpoint for CrossRef
`seqSets.crossRef.databaseName`	String		The database name for CrossRef
`seqSets.crossRef.email`	String		The email address associated with the CrossRef account
`seqSets.crossRef.organization`	String		The organization name for CrossRef
`seqSets.crossRef.hostUrl`	String		The host URL for CrossRef callbacks
`gitHubMainUrl`	String	”https://github.com/loculus-project/loculus”	The link that the GitHub icon in the footer points to

Website Settings

Field	Type	Default	Description
`website`	Object		Website specific setting
`website.websiteConfig`	Object		Settings for the `website_config.json`
`website.websiteConfig.enableLoginNavigationItem`	Boolean	true	Whether the website should show the login button.
`website.websiteConfig.enableSubmissionNavigationItem`	Boolean	true	Whether the website should show “Submit” link in the top navigation bar.
`website.websiteConfig.enableSubmissionPages`	Boolean	true	Whether to completely disable submission related pages. Setting this to false is useful when hosting Loculus for analysis-only purposes.
`website.runtimeConfig.public`	Object		Settings for the `public` section of the `runtime_config.json`
`website.runtimeConfig.public.backendUrl`	String	true	Overwrite the URL where the client-side website code expects the Loculus backend
`website.runtimeConfig.public.keycloakUrl`	String	true	Overwrite the URL where the client-side website code expects the Keycloak
`website.runtimeConfig.public.lapisUrlTemplate`	String	true	Overwrite the URLs where the client-side website code expects the LAPIS instances. Must contain `%organism%` as a placeholder.

User registration and authentication

Field	Type	Default	Description
`auth`	Object		User authentication (Keycloak settings)
`auth.smtp`	Object		Configuration for email sending
`auth.smtp.host`	String		SMTP server hostname
`auth.smtp.port`	Integer		SMTP server port
`auth.smtp.user`	String		SMTP username for authentication
`auth.smtp.replyTo`	String		Reply-to email address for sent emails
`auth.smtp.from`	String		From email address for sent emails
`auth.smtp.envelopeFrom`	String		Envelope from address for sent emails
`auth.verifyEmail`	Boolean	true	If true, requires email verification for new accounts
`auth.resetPasswordAllowed`	Boolean	true	If true, allows users to reset their passwords
`auth.registrationAllowed`	Boolean	true	If true, allows users to register new accounts in Keycloak.
`insecureCookies`	Boolean	false	If true, allows insecure cookies.
`registrationTermsMessage`	String	`"You must agree to the <a href='http://main.loculus.org/terms'>terms of use</a>."`	Message displayed during user registration, typically including terms of service.

Database deployments

Field	Type	Default	Description
`runDevelopmentMainDatabase`	Boolean	true	If true, runs a development database within the cluster.
`runDevelopmentKeycloakDatabase`	Boolean	true	If true, runs a development Keycloak database within the cluster.
`developmentDatabasePersistence`	Boolean	true	If true, makes the database on the argocd preview persistent.

For production environments, these should always be set to false. Instead, external managed databases should be used.

Services

Field	Type	Default	Description
`disableWebsite`	Boolean	false	If true, disables the frontend website deployment.
`disableBackend`	Boolean	false	If true, disables the backend API deployment.
`disablePreprocessing`	Boolean	false	If true, disables preprocessing pipelines.
`disableIngest`	Boolean	false	If true, disables ingestion services.
`disableEnaSubmission`	Boolean	false	If true, disables ENA (European Nucleotide Archive) submission service.
`customWebsiteImage`	String		Optional custom Docker image for the website.

Organism Configuration

Field	Type	Default	Description
`organisms`	Object		An object where the keys are the organism IDs and values are an Organism (type)

Organism (type)

Each organism object has the following fields:

Field	Type	Description
`schema`	Schema (type)
`preprocessing`	A list of Preprocessing (type)	Configuration for the preprocessing pipeline(s)
`ingest`	Ingest (type)	Configuration for the ingest pipeline(s)
`referenceGenomes`	Object	Reference genome sequences for the organism
`referenceGenomes.nucleotideSequences`	Array of NucleotideSequence (type)
`referenceGenomes.genes`	Array of Gene (type)

Schema (type)

Field	Type	Default	Description
`organismName`	String		Display name for the organism
`image`	String		URL to an image that will be shown on the landing page
`loadSequencesAutomatically`	Boolean	true	Whether sequences be loaded automatically on the sequence details page , rather than users having to press a button to do so. (For small genomes, this should probably be true.)
`description`	String
`metadata`	Array of Metadata (type)		Metadata fields associated with the organism.
`earliestReleaseDate`	Object		Configuration object for enabling and configuring the `earliestReleaseDate` metadata field. For each version of an accession, the `earliestReleaseDate` is calculated as the earliest date of the internal release date, the dates in the configured `externalFields` and the value from the previous version of the accession (if there is one). This can be used when having a mix of sequences imported from other databases, as well as sequences released first in this Loculus instance, to have a field that shows the earliest release date regardless of where the sequence was first released.
`earliestReleaseDate.enabled`	boolean		Whether to enable the `earliestReleaseDate` metadata field.
`earliestReleaseDate.externalFields`	Array of strings		Field names to use when calculating the earliest release date. The fields need to be nullable strings formated with `yyyy-mm-dd`.
`website`	Object		Configuration for how the organism data is displayed on the website
`website.tableColumns`	Array of Strings		Columns to display in the browse table
`website.defaultOrderBy`	String		Default column to sort the browse table
`website.defaultOrder`	”ascending” \| “descending”		Default order direction
`silo`	Object		Configuration regarding the SILO database engine
`silo.dateToSortBy`	String		Name of a field of type date. This might speed up date range searches on this field and improve sequence compression.
`silo.partitionBy`	String

Metadata (type)

Field	Type	Description
`name`	String	Key used across app to refer to this field
`displayName`	String	Name displayed to users
`type`
`header`	String	Grouping of fields in sequence details UI
`required`	Boolean	Whether the field is required by backend
`noInput`	Boolean	Whether a field with this name is expected as possible input, and so should be included in the metadata template and as a form field. (If set to true it will not be included).
`generateIndex`	Boolean	Whether the field should be indexed for search. This is only allowed for string fields and facilitates faster filters. It is recommended if the number of different values is rather small.
`columnWidth`	Number	The minimum column width for this field on the search table.
`order`	Number	Order for the column in the search table, lower first
`autocomplete`	Boolean	Whether autocomplete should be offered for the field. This is only allowed for string fields and probably `generateIndex` should be true.
`enableSubstringSearch`	Boolean	If true, search results will contain results that contain the given value as a substring. If false (the default), only exact matches will be returned. This only works for string fields, and you cannot also enable `autocomplete`.
`rangeSearch`	Boolean	If true, enables range search for numeric fields.
`rangeOverlapSearch`	Object	The config settings for enabling range overlap search.
`rangeOverlapSearch.rangeId`	String	The range that this field belongs to. Two fields (the upper and lower bound) need to be defined with the same range ID.
`rangeOverlapSearch.rangeDisplayName`	String	The display name of the range.
`rangeOverlapSearch.bound`	”lower” \| “upper”	Whether this field is the lower or upper bound of the range.
`initiallyVisible`	Boolean	If true, the field is initially visible in the UI.
`hideOnSequenceDetailsPage`	Boolean	If true, hides the field on the sequence details page.
`perSegment`	Boolean	Whether this is a metadata field that should exist for each segment. If so fields will be created as `fieldName_A`, `fieldName_B` in the case of an organism with segments `A` and `B`.
`customDisplay`	Object	Custom display of the field on the sequence details page
`customDisplay.type`
`customDisplay.url`
`ontology_id`	String
`definition`	String
`guidance`	String
`example`	String	Example value for the field.
`ingest`	String	Which NCBI field to map to this field
`preprocessing`	Object	The values of this field will be added to the preprocessing pipeline config file and the available values depend on the chosen pipeline. For the Nextclade pipeline, please see here.

Preprocessing (type)

Field	Type	Description
`version`	Integer	Version of the preprocessing pipeline
`image`	String	Docker image for the preprocessing pipeline
`args`	Array of strings	Arguments passed to the preprocessing pipeline
`configFile`	Object	Fields that should be added to the preprocessing pipeline config file

The values for args and configFile depend on the used preprocessing pipeline. For the Nextclade preprocessing pipeline, please see here.

Ingest (type)

Field	Type	Default	Description
`image`	”ghcr.io/loculus-project/ingest”		Docker image for the ingest pipeline
`configFile`	Object		Fields that should be added to the ingest pipeline config file

The values for configFile depend on the used preprocessing pipeline. For our ingest pipeline which downloads data from NCBI GenBank using NCBI Datasets, the config file needs to contain the taxon_id of the organism and additionally, if the organism is multi-segmented, it requires a list of segment names (nucleotide_sequences) and the nextclade_dataset that can be used for segment identification and alignment.

NucleotideSequence (type)

Field	Type	Description
`name`	String	Name of the sequence
`sequence`
`insdcAccessionFull`	String	INSDC accession of the sequence

Gene (type)

Field	Type	Default	Description
`name`	String		Name of the sequence
`sequence`