GitPod Setup
To get you started, we pre-configured a GitPod [1] environment with Biodepot-workflow-builder (Bwb) and a test RNA-sequencing (RNA-seq) workflow so that you can run the RNA-seq workflow on the web without any set up on your local computer.
How to run our pre-configured environment on GitPod?
To run this demo you will need a connection to the internet, a web browser, and a GitHub account. You don't need any credit card to use GitPod, and can get 50 hours per month for free. See here if you'd like to learn more.
- Run this workflow form GitPod:
- When opening the GitHub demo, please log into your GitHub account to be granted access to GitPod’s services.
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This should bring up the following screen:
Make sure the Autostart option is not checked. Leaving Autostart unchecked will allow you to see these drop-downs every time you start a new GitPod instance.
There will be several drop-downs to select from. You don’t need to worry about these for the demo. Depending on the workflow you chose to run, you might need to change these options in the future.
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Click on the Continue button to proceed to the GitPod IDE, as shown in the following screenshot:
Bwb auto-starts with Docker, please wait until Bwb starts before attempting to open Bwb. GitPod will take about a minute or two to install Bwb.
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Once the terminal stops scrolling during the Docker install of Bwb, click on the Ports tab above the terminal window which is right next to the Terminal tab. You should see a table with the following headers Port, Address, and State. There should be several entries in the table.
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Click on the URL that is associated with port 6080 in the Address column to open Bwb in a new browser tab. If a new browser window/tab does not open, make sure to uncheck the "Block pop-up windows" in your browser's security panel. Alternatively, at the end of the Address column for the same entry, click on the globe icon, and this will open Bwb in a new browser tab. If your browser window is slim, the URL might now show, in which case the globe icon will still be displayed.
Note
If using the Firefox browser, the window that opens after clicking on the globe icon may be caught as a pop-up. When this happens, click on the pop-up blocker icon, then “Allow” the pop-up to be displayed.
Bwb has been extensively tested on Chrome and Firefox. Our tools are not yet optimized for mobile devices.
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Congratulations! You have now successfully deployed the Bwb on GitPod, as shown in the following screen.
Stop/Delete your instance when done
To avoid consuming your free hours on GitPod, you will want to stop or delete your instance when you are done. Your workspace will also stop automatically if left inactive (see GitPod documentation).
Stop GitPod Instance - To stop the GitPod instance, click the button with three horizontal lines (hamburger button) in the upper-left corner of the browser window. This will bring up a drop-down menu. Click on the menu option that says Gitpod: Stop Workspace. This will stop the workspace. The same workspace can be relaunched by following this LINK, selecting the GitPod instance at the top, and selecting Open from the options button, which is 3 black dots stacked vertically. GitPod does not provide a way to differentiate between instances besides showing which was most recently running.
Delete GitPod Instance - To delete a GitPod instance, stop the instance following the previous instructions. When the instance stops, click the gray “Go to Dashboard” button to access the GitPod dashboard (or follow this LINK). You will see a list of your most immediately opened GitPod instances. Click the options button (3 black dots stacked vertically), on the far right of a GitPod instance. In the resulting drop-down menu, click on the red Delete text. You will be prompted with a new window. Click the red button that says Delete Workspace.
Resize Bwb Window - To auto resize the Bwb window in the browser, this will require editing the url in the address bar. If you're working on a workflow with changes, save the changes first as resizing will cause Bwb to reset. The current url should be something like this http://example_address/vnc.html?autoconnect=1, edit the address to http://example_address/?auto and press the enter key. After a few seconds Bwb will reload at the current size of your browser window.
Prevent Workspace Timeout - GitPod has a timeout function. If no changes are made through the GitPod IDE of the launched workflow, the GitPod workspace could automatically close in 30 minutes or less. To prevent a timeout from happening, simply open a new terminal tab in the GitPod IDE, and execute a simple command like "ls". Repeat the command every 20 minutes or so to prevent a timeout while running a long workflow.
Troubleshooting
Ports tab doesn't show - If the port tab doesn't show, there may be a conflict with browser plugins or other tabs open. Try restarting your browser and opening the GitPod instance without other tabs open.
Bwb shuts down when loading workflow - When opening a workflow on GitPod, sometimes Bwb will not re-launch with the workflow. If this happens, right click the desktop, select "Bwb" and load the workflow again.
Bwb does not load on start - When opening the Bwb window on GitPod, sometimes Bwb will not have started. If this happens, right click the desktop, select "Bwb" and load the workflow again.
Follow this link for additional troubleshoot tips.