pupster90/combat-seq repository overview

⁠HarmonyRNA Docker Tutorial

This tutorial is for people interested in the HarmonyRNA⁠ project. We explain how to run the website locally so that you can make changes to the code. Docker⁠ is by far the easiest way to work on this project. Docker has quickly become one of the most popular ways to share code, because it makes it easy to run any code on any computer.

⁠Step 1: Install Docker

You can quickly run HarmonyRNA code on Linux/Mac/Windows using docker. install docker here⁠. We recommend watching a docker tutorial and installation video on youtube⁠.

⁠Step 2: Download and Run Covid Counties

Once you have docker, open your computer terminal and run the following code to download the HarmonyRNA project:

docker pull pupster90/combat-seq

The above code installs the HarmonyRNA docker image on to your computer. Run this next line to start RStudio⁠ in your browser:

docker run -d -e PASSWORD=harmonyrna --user root --name harmonyrna -p 80:8787 -p 8888:8888 pupster90/combat-seq /init

⁠Step 3: Run HarmonyRNA Locally

Open an internet browser (chrome, safari,...). Go to the url localhost. You will be asked to sign into Rstudio. Sign in with username rstudio and password harmonyrna. You now have access to the Rstudio environment where you can run HarmonyRNA code.

You will see all of the source code in the HarmonRNA Github⁠ repository. With the app.R file selected, click Run App to start running the HarmonyRNA website locally. Go to localhost:8888 to view the website. app.R is the most important file. Read it first to begin changing code.

⁠Step 4: Contact Us

If you are another lab interested in HarmonyRNA, we are happy to have you reach out to Atul Butte's lab⁠. Sanchita Bhattacharya is the senior scientist and manager of this project (email: [email protected]⁠). If you are a programmer with technical questions please reach out to the senior programmer of HarmonyRNA, Matthew Elliott (email: [email protected]⁠). We look forward to hearing from you!