AXIOME3 Web Application Wiki

Prerequisites

1. Docker (1.13.0+) https://docs.docker.com/get-docker/
2. Docker-compose (3.0+) https://docs.docker.com/compose/install/

Email Notification

You will need a gmail credential to use the email notification service. Due to security reason, we purposely do not make the credential file publicly available. If you wish to use this service, please send an email to [email protected] asking for the credential file.

After receiving the credential file, place this file in the backend directory to use the email notification service.

Installation and Usage

If you wish to install AXIOME3 in the remote server that is accessible via SSH, please take a look at Accessing the app installed in the remote server section for more details.

Installation and Termination

1. Clone this repository (to the location you want to install the application)

   git clone https://github.com/neufeld/AXIOME3-GUI.git

2. Run the following command to install and launch AXIOME3-GUI app. This may take some time to run if running for the first time.

   Make sure AXIOME3-GUI is not already running!

   Note that once the above command is run, it will create and save Docker images. After the first installation, you can launch the app with the same command (it will take much less time since the app is already installed.)

   docker-compose -f docker-compose_production.yml up -d

   The above command will launch the app in the background.

   If you want to launch the app in the foreground, use the following command instead. (you will see verbose messages if running in the foreground)

   docker-compose -f docker-compose_production.yml up

3. To cleanly exit the app, run the following command. (If running the app in the foreground, press CTRL+c to terminate the app first.)

   docker-compose -f docker-compose_production.yml down

4. Then, remove Docker data volumes used in AXIOME3-GUI by running the command,

   docker volume prune

5. If you wish to uninstall the app, run the following command. It will remove AXIOME3-GUI Docker images. (you may need sudo/admin privilege)

   docker image rm axiome3-gui_app axiome3-gui_backend axiome3-gui_pipeline_worker axiome3-gui_extension_worker

Usage

1. Open web browser (currently supports Chrome, Edge, Firefox), and navigate to localhost:8080 in the address bar.

2. A detailed usage tutorial can be found here.

Note: There are some known installation bugs. See the "Known Issues" section for dealing with the bugs if you ever encounter one

Accessing the app installed in the remote server

Note that you need to be able to access server or compute cluster via ssh!

If using SSH command to access server

1. Access remote server or cluster with port forwarding enabled by adding -L flag to the ssh command. (other flags can also be added if needed)

ssh -L 8080:localhost:8080 USERNAME@REMOTE_SERVER (-L 8080:localhost:8080 forwards the remote port 8080 to local port 8080)

Make sure other apps ARE NOT running on port 8080 on local PC and remote server!

2. Navigate to the direcory to install AXIOME3-GUI application.

3. Install AXIOME3-GUI application as described in Installation and Usage section.

4. On your local PC, open web browser, and navigate to localhost:8080 to use AXIOME3.

If using PuTTY to access the server

1. Expand the SSH tab by clicking on the + sign

2. Click on Tunnels tab

3. In the Source port, enter 8080. In the Destination, enter 127.0.0.1:8080. Click Add to add this tunnel

4. Go back to the Session tab, and save this setting (either overwrite to existing one, or save it as a new session), so that you don't have to do this every time you want to use AXIOME3 GUI.

Known Issues

Please take a look at Known Issues section for more details.

Collaboration

Please refer to Collaboration section for more details.