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This page helps you to configure Cloudgene and describes all parameters of the settings.yamlfile. When you change a parameter in the file, you have to restart your Cloudgene instance to see the change in action.

Database connection

Cloudgene uses an embedded H2 database to store meta data about jobs and users:

  driver: h2
  database: data/cloudgene
  user: cloudgene
  password: cloudgene

For production we recommend to use a MySQL database:

  driver: mysql
  host: localhost
  port: 3306
  user: cloudgene
  password: cloudgene

Mail Server

If no mail server is set, new registered users are activated immediately and no confirmation links are sent. This can be activated by defining a local or remote SMTP mail server:

  smtp: localhost
  port: 25
  user: username
  password: password
  # the email address that Cloudgene uses to send emails


Change the name of your service. If you plan to run Cloudgene on a sub-directory, then you can change the url-prefix.

# the name of your service [default: Cloudgene]
name: My Service
# port [default: 8082]
port: 8082
# max file size that can be uploaded in Bytes. -1 is unlimited [deafult: -1]
uploadLimit: 50000
# root url of the web-application [default: empty]
urlPrefix: /my-service

HTTPS Certificate and Security

Activate secure Cookies and use your own SSL Certificate to secure your connection:

# use https with the provided key store [default: false]
https: true
httpsKeystore: /your/key.jks
httpsPassword: password
# use secure cookies [default: false]
secureCookie: true
# use this secret key to generate JWT tokens.
# please use a secret random string
secretKey: some-random-string

More about on how to setup a java Keystore can be found here.

Directories and Workspace

If your service produces a lot of data, it could be useful to set the workspace directories to an other disc. The following directories can be changed:

# location for temporary files (e.g. cached file uploads) [default: tmp]
tempPath: tmp
# location for the results of a job [default: workspace]
localWorkspace: /mnt/new-disc/workspace
# HDFS location for the results of a job [default: cloudgene/data]
hdfsWorkspace: cloudgene/data
# if set all HDFS files are deleted after job execution [default: true]
removeHdfsWorkspace: true
# HDFS location for the meta-data of an app [default: cloudgene/apps]
hdfsAppWorkspace: cloudgene/apps


For security reasons, files can be downloaded 10 times. Users will get an error message, when this number is succeeded. The maximal number of downloads can be increased or set to -1 in order to allow unlimited downloads:

# max number of downloads [default: 10]
# use -1 for unlimited downloads
maxDownloads: 10

Download counters can also be deactivated for specific jobs in the Admin Panel.


Cloudgene manages two different queues to execute setup steps and workflow steps for a job. The number of jobs which are executed in parallel can be set for each queue independently:

# max. n jobs can execute their setup steps in parallel [default: 5]
threadsSetupQueue: 5
# max. n jobs can execute their workflow steps in parallel  [default: 5]
threadsQueue: 5
# each user can run max. n jobs at the same time  [default: 2]
maxRunningJobsPerUser: 2


To change the default values please adapt the following parameters in your settings.yaml file:

# retire jobs after x days [default: 6]
retireAfter: 6
# sent notification after x days [default: 4]
notificationAfter: 4
# perform retire as a cronjob [default: false].
autoRetire: true
# perform retire cronjob every x hours [default: 5].
autoRetireInterval: 5


If autoRetire is set to false, you have to click on the Retire button in Administrator Dashboard to clean up.