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Connecting openBIS and Galaxy: from lab data to analysis and back

Browse openBIS files in Galaxy, analyse them, and return results to your lab notebook

Polina Polunina
interoperability
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Lab data and analysis often live in different places. An experiment is documented in openBIS, while its data are analysed in Galaxy. Moving files between them manually adds extra downloads and uploads to the workflow.

openBIS combines an electronic lab notebook, inventory management, and research data management. A new repository plugin for openBIS in Galaxy connects these two environments. It lets you browse files from openBIS inside Galaxy, import them into a history, and send analysis results back to an existing Collection or Object in openBIS.

The integration supports importing existing openBIS DataSet files and importing or exporting files through AFS, the storage used by openBIS 7’s Files tab. Access follows your openBIS account’s permissions. If openBIS is not listed under Manage Your Repositories when creating a connection in Galaxy, ask your Galaxy administrator to enable the integration.

Connect your openBIS account

You need an openBIS account with access to the data you want to analyse, a Personal Access Token (PAT), and a Galaxy account on a server with the integration enabled.

Create a PAT using the openBIS v3 API, or ask your openBIS administrator for help.

In Galaxy, open your user preferences and select Manage Your Repositories, then Create and openBIS. Give the connection a descriptive name and provide:

  • Your openBIS base URL, such as https://openbis.example.org.
  • Your Personal Access Token.
  • Writable enabled if you want to export results; it is disabled by default.
  • Verify TLS certificates enabled to verify the server’s identity.

Connect Galaxy to openBIS using a personal access token.

Bring lab files into a Galaxy history

Open Upload, choose Choose remote files, and select your openBIS connection. Browse through your Space, Project, and Collection to find the files you need. Objects inside Collections are also shown as folders. In the openBIS API, Collections are called Experiments and Objects are called Samples.

The file source exposes two kinds of storage:

  • AFS files appear inside a Collection’s or Object’s files folder. They can be imported and, when writing is enabled, used as export destinations.
  • Existing openBIS DataSets can be browsed and downloaded, but are read-only through this integration.

AFS is the file storage introduced in openBIS 7 and used by its Files tab. The openBIS documentation recommends AFS for new uploads. An openBIS DataSet is a registered bundle of files, not the same concept as an individual dataset in a Galaxy history.

Select a file and start the import. Once it is ready in your history, you can use Galaxy tools and workflows as usual.

Import paired-end FASTQ files from openBIS into Galaxy.

Send results back to openBIS

Open Galaxy’s Export datasets to repositories tool (export_remote) and select your output dataset. Use the destination browser to select the existing Collection’s or Object’s files directory, or a subfolder inside it, and run the export.

Return to openBIS and refresh the entity’s Files tab to see the result alongside your input data. Use a clear, distinct output name so it is easy to identify what came back from Galaxy.

Export FastQC reports from Galaxy back to the original openBIS record.

This is an explicit file-transfer workflow, not automatic synchronization. Exporting a result does not automatically copy Galaxy’s workflow or provenance into openBIS metadata; the analysis history remains in Galaxy.

A few things to know

  • The browser shows all Spaces your token can access, not just your home Space. A shared Space such as ELN_SETTINGS may therefore also appear.
  • Create Spaces, Projects, Collections, and Objects in openBIS before using them from Galaxy. The integration can create AFS folders, but not openBIS entities.
  • Curently we follow the Collection-based hierarchy in our openBIS implementation. Objects outside Collections, classic Attachments, and linked/container DataSets are not covered by this browsing workflow.
  • Renaming and deleting AFS files are not possible; manage those operations in openBIS.