Carpentries @ Oklahoma State University: Resources for online workshops

We are currently running everything through the OSU High Performance Computing Center during our online classes, so downloading software is not necessary. However, you do have the option of downloading Anaconda and running the Jupyter Notebooks on your own machine (so you can save changes and create your own Notebooks). In order to run R, you must also install R.

Download Anaconda to run Jupyter Notebook 

1. Download and install Anaconda: https://docs.anaconda.com/anaconda/install/

2. Go to https://www.r-project.org/ to download R. Click on CRAN (Comprehensive R Archive Network) under Download, and scroll down to your country. Select the download link corresponding to the city that is geographically closest to you. Open the file and install.

3. Install IR kernel:

•  On PC, search for Anaconda Prompt in the menu in the bottom left of your Windows desktop. Right click the icon, and choose Run As Adminstrator. In the prompt, type conda install -c r r-irkernel. During the installation process, Anaconda might ask if you want to proceed ([y]/n)?` Just type y.
• On Mac, open Terminal. Type conda config --add channels r and press enter. Then type conda install --yes r-irkernel and press enter.

4. Following these instructions, open Anaconda and select Environments to create an new environment. Click Create.

5. In Name, type my_r_environment. Next to Packages, select Python 3.7 and R. Select r from the dropdown menu. Click Create.

6. Click the arrow next to my_r_environment and select Open with Jupyter Notebook. It will open in your default web browser.

7. You can download the IPYNB files from your Carpentries workshop. Go to the workshop notebooks on TIGER and login using the same workshop credentials.  Select all the notebooks and then right click.  Select Download.  Then go to your local copy of Jupyter Notebook and open it.  It will be inside the Anaconda folder.  Create a folder (yearmodate_workshop_notebooks) and open it.  There is an upload button on the upper right corner.  Click it and select the notebooks that were downloaded.  Click on Open and then on the blue Upload buttons inside of the Jupyter Notebook folder that you created.  For the data files, use the "New" button, also in the upper right hand corner, and select folder.  Label the folder as "Data" and open it.  Now download the data files and go to the "Data" folder.  Click upload and select the files that you downloaded (csv).  Now you should have all the notebooks and the data files from the workshop ready to use on your own device.
 

Downloading R and R Studio to open Rmd files.

1. Go to https://www.r-project.org/ to download R. Click on CRAN (Comprehensive R Archive Network) under Download, and scroll down to your country. Select the download link corresponding to the city that is geographically closest to you. Open the file and install.
2. Go to https://www.rstudio.com/products/RStudio/#Desktop to download the RStudio desktop software. Open the file and install.