##### The filesystem location where files managed by irida are stored. The platform ##### will *NOT* automatically make this directory, so it must exist before you ##### start any instance of the platform. sequence.file.base.directory=/opt/irida/data/sequence reference.file.base.directory=/opt/irida/data/reference output.file.base.directory=/opt/irida/data/output assembly.file.base.directory=/opt/irida/data/assembly pipeline.plugin.path=/etc/irida/plugins ##### Set the max upload size (in bytes). If left unconfigured, the max upload ##### size is unlimited (or limited by the container hosting IRIDA). # file.upload.max_size= ##### Set number of threads for FASTQC and file post-processsing. The max size ##### should not be more than the number of jdbc threads. file.processing.core.size=4 file.processing.max.size=8 file.processing.queue.capacity=512 file.processing.process=true ##### OAuth2 JWT security settings. # Default keystore for holding public/private keys required for OAuth2 JWK Access Token encryption/decryption oauth2.jwk.key-store=/etc/irida/jwk-key-store.jks oauth2.jwk.key-store-password=SECRET ##### The database-specific settings. Several examples of how to specify a ##### Hibernate driver are listed below (but commented out). ## MySQL (or MariaDB) spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver spring.jpa.database-plaform.dialect=org.hibernate.dialect.MySQL55Dialect # Deprecated as of 22.01 #jdbc.driver=com.mysql.jdbc.driver #hibernate.dialect=org.hibernate.dialect.MySQL55Dialect ## Database location (you may need to use a different string for different ## database vendors). spring.datasource.url=jdbc:mysql://localhost:3306/irida_test # Deprecated as of 22.01 #jdbc.url=jdbc:mysql://localhost:3306/irida_test ## Connection settings: spring.datasource.username=test spring.datasource.password=test # Deprecated as of 22.01 #jdbc.username=test #jdbc.password=test ## Configuring Liquibase to execute a schema update. Should only make changes to ## the database when executing the first time, or when upgrading. liquibase.update.database.schema=true ## Configure Hibernate to execute a schema construction. WARNING: do not use this ## at the same time as the Liquibase schema update. Liquibase will *not* execute ## if this value is set, warnings will be produced in the log. These settings should ## only be used in a development environment (**not** production). spring.jpa.hibernate.ddl-auto= spring.jpa.properties.hibernate.hbm2ddl.import_files= # Deprecated as of 22.01 #hibernate.hbm2ddl.auto= #hibernate.hbm2ddl.import_files= ## Configure Hibernate to show SQL in the log file. You *probably* don't want ## to enable this, but could be useful for debugging. spring.jpa.show-sql=false # Deprecated as of 22.01 #hibernate.show_sql=false ## Connection Pool settings: spring.datasource.dbcp2.intial-size=10 spring.datasource.dbcp2.max-active=20 spring.datasource.dbcp2.test-on-borrow=true spring.datasource.dbcp2.test-on-return=true spring.datasource.dbcp2.test-while-idle=true # Deprecated as of 22.01 #jdbc.pool.initialSize=10 #jdbc.pool.maxActive=20 #jdbc.pool.testOnBorrow=true #jdbc.pool.testOnReturn=true #jdbc.pool.testWhileIdle=true ## Configure the JDBC library to use this query to verify that a managed ## connection is still valid. This may need to change, depending on your database vendor. spring.datasource.dbcp2.validation-query=select 1 # Deprecated as of 22.01 #jdbc.pool.validationQuery=select 1 spring.datasource.dbcp2.max-wait=10000 spring.datasource.dbcp2.remove-abandoned=true spring.datasource.dbcp2.log-abandoned=true spring.datasource.dbcp2.remove-abandoned-timeout=60 spring.datasource.dbcp2.max-idle=10 # Deprecated as of 22.01 #jdbc.pool.maxWait=10000 #jdbc.pool.removeAbandoned=true #jdbc.pool.logAbandoned=true #jdbc.pool.removeAbandonedTimeout=60 #jdbc.pool.maxIdle=10 ## Configure the password expiry time in days. A value of -1 will set no expiry. security.password.expiry=-1 ############################################################################### # Execution Manager configuration Galaxy. This is how IRIDA should connect to # # the internally managed instance of Galaxy for executing workflows. # ############################################################################### # The URL for the Galaxy execution manager galaxy.execution.url=http://localhost/ # The API key of an account to run workflows in Galaxy. # This does not have to be an administrator account. galaxy.execution.apiKey=xxxx # The email address of an account to run workflows in Galaxy galaxy.execution.email=user@localhost # The data storage method for uploading data into a Galaxy execution manager. galaxy.execution.dataStorage=local ################################## # Workflow configuration options # ################################## # The timeout (in seconds) for uploading files to Galaxy for execution # Increase this value if uploading files to Galaxy is timing out. #galaxy.library.upload.timeout=300 # The polling time (in seconds) for checking if files have been uploaded to Galaxy # This value should not be greater than $galaxy.library.upload.timeout #galaxy.library.upload.polling.time=5 # Number of threads used to wait for completion of uploading files. #galaxy.library.upload.threads=1 # Maximum number of workflows IRIDA will schedule to run at the same time irida.workflow.max-running=4 # The number of threads used to handle analysis tasks (e.g., submitting files to Galaxy and downloading results). # If the maximum number of workflow threads is large, it may improve performance to increase this value as well. #irida.scheduled.analysis.threads=4 ################################## # Analysis configuration options # ################################## # The number days before intermediate files for an analysis get cleaned up. # That is, the number of days before files in Galaxy get deleted for the analysis. # Leave commented out for no cleanup. # This value can be fractional representing a fraction of a day (e.g. 0.5 for half a day). #irida.analysis.cleanup.days= ################################# # Scheduled Task configuration # ################################# #Cron string for how often the email subscriptions are sent out. #Format: sec min hrs dom mon dow irida.scheduled.subscription.cron=0 0 0 * * * irida.scheduled.threads=2 ################################# # NCBI SRA Export configuration # ################################# #Host to upload ncbi exports ncbi.upload.host=localhost #FTP Username and password for bulk SRA uploads ncbi.upload.user=test ncbi.upload.password=password #base directory in which to create SRA submissions ncbi.upload.baseDirectory=tmp #port for ftp upload ncbi.upload.port=21 #Default namespace to preface file identifiers ncbi.upload.namespace=IRIDA # Adjusts Control Keep Alive Timeout value, which can assist in keeping an FTP connection alive for long file transfers. # See . #ncbi.upload.controlKeepAliveTimeoutSeconds=300 #ncbi.upload.controlKeepAliveReplyTimeoutMilliseconds=2000 # Adjusts whether or not to use active vs passive mode for the FTP connection. # Passive mode is recommended if you are behind a firewall/NAT. #ncbi.upload.ftp.passive=true # A list of workflow types to disable from display in the web interface # For example `irida.workflow.types.disabled=ASSEMBLY_ANNOTATION,ASSEMBLY_ANNOTATION_COLLECTION,BIO_HANSEL,MLST_MENTALIST,REFSEQ_MASHER,SISTR_TYPING,PHYLOGENOMICS` # If you wish to re-enable any default disabled pipelines, you can set this to an empty value (i.e., irida.workflow.types.disabled=) # If you wish to keep the default disabled pipelines but include additional pipelines, you can set to (irida.workflow.types.disabled=SISTR_TYPING,MLST_MENTALIST) and include your own after this list. #irida.workflow.types.disabled=