Workflows in Rbbt

Workflows in Rbbt are installed in predefined locations. The default location is ~/.rbbt/workflows but it can be redefined with a different directory by placing it on ~/.rbbt/etc/workflow_dir. You can place the workflow in the directory manually, or you can install it automatically from source using the following command:

rbbt workflow install <workflow>

This command will download the workflow from http://github.com/Rbbt-Workflows. It will also update the workflow to the latest git revision. You can see a list of installed workflows doing rbbt workflow list.

To use the workflow you can again use the rbbt command: rbbt workflow task <workflow>. Issuing that command will list the available tasks for the workflow. You can then do rbbt workflow task <workflow> <task> -h to learn how to use each particular task.

Workflows may require extensive resources, such a genomics data, fast access key-value stores, caches, indices, etc. These get created on demand. In order to help the initial process, some workflows include a bootstrap script, that will issue a number of jobs that will prompt the installation of this infrastructure. Workflow commands are issued using the rbbt command: rbbt workflow cmd <workflow> will list the available commands for that workflow. To issue the bootstrap do rbbt workflow cmd <workflow> bootstrap.

To cut down setup time even more, you can configure remote file servers to gather resources from an already configured server. See the installation instructions for more information.

In the cases where the setup of the workflows infrastructure becomes to costly, you may also configure a remote workflow. This will forward all work transparently to the remote server. This is specially recommended for the MutEval workflow, which uses the dbSNFP resource for protein mutation damage predictions, and is over thirty gigabytes in size.

File servers and remote workflows are served from any Rbbt REST server. Currently you may use https://rbbt.bsc.es.

You may start you own REST interface for a workflow issuing the following command rbbt workflow server <workflow>.