https://github.com/stuartmac/jalview-in-docker
Run Jalview GUI in Docker
https://github.com/stuartmac/jalview-in-docker
Last synced: 5 months ago
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Run Jalview GUI in Docker
- Host: GitHub
- URL: https://github.com/stuartmac/jalview-in-docker
- Owner: stuartmac
- Created: 2025-04-18T13:14:01.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-18T14:13:35.000Z (about 1 year ago)
- Last Synced: 2025-04-19T03:39:05.984Z (about 1 year ago)
- Language: Dockerfile
- Homepage:
- Size: 3.91 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# Jalview Docker (GUI for macOS via XQuartz)
Run Jalview in a clean Linux environment via Docker with X11 forwarding to macOS.
## Prerequisites
- macOS with [XQuartz](https://www.xquartz.org/) installed
- Docker Desktop for Mac
- Run `xhost + 127.0.0.1` in Terminal after starting XQuartz (you may also need to run `export DISPLAY=:0` before `xhost`)
## Additional XQuartz Settings
XQuartz should be configured with the following settings:
1. Open XQuartz and go to `Preferences` (Command + ,).
2. Under the `Security` tab, ensure the following options are checked:
- `Allow connections from network clients`
3. It's good to restart XQuartz.
## Build
```bash
docker build -t jalview-gui .
```
## Run
```bash
docker run -e DISPLAY=host.docker.internal:0 \
-v $PWD:/data \
--rm jalview-gui
```
## Integrating Jalview with a Slivka Stack
This Docker setup is especially useful for integrating Jalview with a containerized Slivka service. By pre-configuring Jalview to connect to your running Slivka instance, you can:
- Use Slivka-exposed tools directly within Jalview
- Customise Jalview’s analysis capabilities by adding compatible tools to your Slivka container
- Rapidly prototype and deploy new bioinformatics tools that are immediately accessible via Jalview’s GUI
This integration is ideal for development environments where you want to test or share new Jalview-compatible services with minimal setup.
## Add Jalview to XQuartz Applications
For easier access, you can add Jalview to the Applications menu in XQuartz:
1. Open XQuartz and go to `Applications > Customize...`.
2. Click the `+` button to add a new application.
3. Set the following:
- **Name**: Jalview
- **Command**: `docker run -e DISPLAY=:0 -v ~:/data --rm jalview-gui`
4. Click `Done` to save the changes.
You can now launch Jalview directly from the XQuartz Applications menu.