Skip to main content

Workspace Export

  • Updated

Workspace Exports are downloadable "snapshots" of the data in your organization's Geneious Cloud or Geneious Biologics Workspace. The Export includes all users' private and shared documents that were present at the time it was prepared. It also preserves folder structure, so that context is maintained.

⚠️ Workspace Exports are intended to be used as a record or for traceability purposes. Please note that they are not intended for backups - an export cannot be used to rollback or restore your workspace. Geneious Cloud already has a built-in internal backup system for unforeseen system-wide events. ⚠️ 
 

Getting Started
Downloading your Snapshots
Extracting your Snapshots
What’s Included in a Snapshot?
Limitations
Feedback & Support
 

Getting Started

Workspace Export generates a snapshot of your entire cloud workspace. This snapshot is stored on our servers and can be downloaded at any time.

To begin:

  1. Ensure you are a Geneious Cloud or Geneious Biologics administrator user, or a user with admin permissions
  2. Visit https://app.geneious.eu/workspace-export or your Geneious Biologics workspace and login.
  3. Click on "Workspace Exports" in the left navigation bar.
  4. Click “Prepare New Export”.

 

This will start a job to create a snapshot of your workspace. Depending on the size of your workspace, the process may take several hours. You can check progress via the Jobs widget in the bottom-left corner. You can safely close your browser or navigate away—the export will continue in the background.

Once completed, a Download button will appear. Clicking it will take you to a page with instructions and links for downloading your data.

Snapshots are shared with all cloud administrators in the workspace. Any admin can create, view, or download snapshots.

 

Downloading your Snapshots

Snapshots are downloaded as multi-part ZIP archives. This ensures even large workspaces can be downloaded reliably. For larger workspaces, multiple files will need to be downloaded.

All parts of a snapshot must be downloaded before extraction will work.

Option 1: Download via Web UI

This is the simplest method:

  1. Open your snapshot in the web UI.
  2. Click Download All.
  3. Wait for all ZIP parts to download to your computer.

Note: Your browser must remain open and connected to the internet during the download. If the process is interrupted, you can restart it later without data loss.

 

Option 2: Download via Python Script (Recommended for large Workspaces)

For large datasets, we recommend using our Python download script. This approach:

  • Doesn’t require a browser
  • Automatically retries on failed downloads and connection interruptions

Follow this guide for full instructions →

 

Extracting your Snapshots

Once all ZIP parts are downloaded, you’ll need to extract them. We recommend using 7-Zip or a similar tool.

Once extracted, the archive recreates your Geneious Cloud folder structure, with each document saved as a .geneious file.

Here's how to extract your snapshot depending on your OS:

Windows

We highly recommend downloading and using the 7-Zip tool on the downloaded zip file. 

macOS

  1. Open Terminal (search for it in Spotlight or find it in Utilities).
  2. Type cd ~/Downloads and press enter.
  3. Type unzip  (with a space after unzip).
  4. Drag and drop the file with the .zip extension into the Terminal window, then press enter.

If you run into issues, we recommend downloading and using 7-Zip.

Linux

We highly recommend downloading and using the 7-Zip tool on your downloaded zip archive. The Info-ZIP unzip utility available in many distros does not (at this time) properly support unzipping of multi-part ZIP archives.

 

What’s Included in a Snapshot?

Each snapshot includes:

  • All visible documents in your workspace, including ones that haven't been explicitly shared with you. The original folder paths of these documents are preserved in the ZIP file structure.
  • Referenced documents that would otherwise not be directly visible in your folder tree.  These will be included in the .geneious file of the documents that reference them.  Such documents that are referenced by multiple other documents may appear in multiple .geneious files. Referenced documents that are directly visible in your folder tree will also appear in their own .geneious file.
  • Geneious Biologics Annotator Results, these documents consist of an annotated sequence list in geneious format, alongside a csv file containing extra table data, such as notes, labels and assay data.

Any documents that were skipped for other reasons, such as errors that occurred during export, should be listed in a SKIPPED_DOCUMENTS.csv file that will be included in the snapshot archive if any documents were skipped that you want. Please include a copy of that file in any support requests that you raise regarding documents that are missing from your snapshot.

Workflows are not included in snapshots at this time.

 

Limitations

  • Each organization is limited to two snapshots at a time.
  • Old snapshots can be deleted to make room for new ones.
  • Snapshots must be unzipped before they can be used in Geneious Prime or other software.

 

Feedback & Support

Workspace Export is actively being improved. If you have suggestions or feature requests, please reach out to our support team.

Related to

Related articles