Loading workflows from GitHub

If additional workflows are required, you can download them using the git command on GitPod. To do this, navigate to your GitPod workspace in the browser and click on the Terminal tab which is right next to Ports. If the terminal pane is running Docker, you will need to open a new terminal tab. To do this, find and click the large “+” button to the right of the Ports tab. A new terminal tab will open, providing access to a new terminal where the git command can be used.

Cloning a git repository containing multiple workflows will be our objective. To accomplish this, we need to enter the following command:

git clone https://github.com/BioDepot/GDC_Genomic_Workflows.git

If we copy/paste the above command, the browser may ask if we want to allow or block access to the clipboard. If we click Allow we will be able to directly access the clipboard and paste the command into the terminal prompt. If we don’t allow access, you will need to type in the above command exactly as you see it. Once we enter the command, a download will occur with output displaying in the terminal window.

Now we can go into Bwb (see GitPod Setup in Episode 1 if you don’t know how to open Bwb) and select a workflow from those that were just downloaded. In Bwb, click on the File menu option and select Load Workflow. A window titled Load Workflow from Directory will pop up with a selection of workflows to load. Double-click on the GDC_Genomic_Workflows folder, double click on the workflows folder, then single-click on the GDC_mRNA_multi_dr32chr22 folder and click Choose in the bottom-right corner of the pop-up. This will load the selected workflow. We have now successfully downloaded a workflow from GitHub and loaded it into Bwb.

https://github.com/BioDepot/GDC_Genomic_Workflows/tree/main/workflows/GDC_mRNA_multi_dr32chr22