Additional Configuration and LimitationsΒΆ

  1. Configuring the query timeout

    You can set the environment variable CLOUDLAUNCH_QUERY_CACHE_PERIOD before starting Galaxy to control the caching period (in seconds). Setting this to 0 will allow you to get around the node removal issue where, if a Pulsar node is removed, jobs may be routed to a dead node for the duration of the caching period. However, we recommend setting a value greater than 0 to avoid repeatedly querying a remote server during each job submission.

  2. Incompatible tools

    Due to the nature of how Galaxy collects metadata on datasets, certain tools are not compatible with job execution in the bursting mode. Some of these issues will be resolved once Pulsar is upgraded to collect metadata itself but for the time being the following is an (incomplete) list of tools and tool classes that will not operate when executed via the GalaxyCloudRunner: upload tool, data managers, tools that use metadata input, and tools that use custom data discovery.

  3. Auto-scaling

    Currently, the GalaxyCloudRunner does not support automatic scaling, you must manually add and remove individual nodes but you can add as many as you would like. We will be adding autoscaling features as part of CloudMan v2.0 in future.

  4. Galaxy versions prior to 19.01

    Galaxy versions prior to 19.01 do not support certain features required by GalaxyCloudRunner and therefore, need more complex configuration steps.