Shesmu is part of a bioinformatics workflow launching system. It does not do workflow launching in the usual sense.

Shesmu acts as an intermediary between two systems: a database of analysis provenance and a workflow scheduler. It scans the provenance system for a list of which files have been produced and then uses decision-action blocks called olives to decide what “actions” should be run. Actions can be launching workflows or filing tickets.

It can filter and aggregate the provenance information to decide what actions to perform. Shesmu is designed to operate in a stateless way. When the server starts up, it creates a list of all actions that need to be performed, then it issues commands to the workflow launcher, which should politely recognise which commands have been previously executed and only launch the new tasks.

Plugins are used to communicate with other systems to perform the real work--Shesmu is an empty vessel that requires plugins to find data and take action. The olives are supplied by a script that is compiled and run over all the provenance data.

Read the Documentation for details on how to use Shesmu, develop plugins, and adminsitrate an instance.

Dependencies

What Shesmu requires will depend on which plugins you enable. Plugins can be disabled by passing -pl "!plugin-foo" to disable a plugin when calling mvn commands.

Build dependencies:

• Java 17 or later
• Maven 3.8 or later
• NPM
• Docker (optional) for container builds

Optional runtime dependencies:

• Prometheus (strongly recommended)
• Prometheus Alert Manager (required for Olive Alert to work)
• JIRA
• GitHub
• GitHub, GitLabs, or BitBucket for storing configuration files (recommended)

For details on building and installing Shesmu, check the installation guide.