diff --git a/learners/files/data_setup.Rmd b/learners/files/data_setup.Rmd
index 1d80c31..cf67761 100644
--- a/learners/files/data_setup.Rmd
+++ b/learners/files/data_setup.Rmd
@@ -5,18 +5,34 @@ You will need to download some example files for this lesson. In this tutorial w
### Setting up a practice Git repository
For this tutorial some existing tools are needed to build the workflow. These existing tools will be imported via GitHub.
-First we need to create an empty git repository for all our files. To do this, use this command:
+
+
+#### Make a repository on GitHub.com
+
+Head to [github.com/new][github_new_repo] and create a new repository.
+
+Name it `novice-tutorial-exercises`.
+
+Make sure the repository is `public`.
+
+Check 'Add a README file', and choose `GNU General Public License v3.0` as your license.
+
+#### Clone the repository
```bash
-git init novice-tutorial-exercises
+git clone git@github.com/YOUR_GITHUB_USERNAME/novice-tutorial-exercises
```
-Next, we need to move into our empty git repo:
+Next, we need to move into our git repo:
```bash
cd novice-tutorial-exercises
```
+
+
+#### Add in bio-cwl-tools as a submodule
+
Then import bio-cwl-tools with this command:
```bash
@@ -25,6 +41,7 @@ git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
+
### Downloading sample and reference data
Create a new directory inside the `novice-tutorial-exercises` directory and download the data:
@@ -61,6 +78,16 @@ We should exclude the rnaseq folder from being tracked in this repository.
echo 'rnaseq/' >> .gitignore
```
+### Add .gitignore to git
+
+`.gitignore` is a file that is tracked like all other GitHub commands.
+
+```
+git add .gitignore
+git commit -m "Don't track files in the rnaseq directory"
+git push
+```
+
### STAR Genome index
@@ -303,4 +330,4 @@ Then retry the `md5sum` command
[dos2unix]: https://phoenixnap.com/kb/convert-dos-to-unix
[checksum_wiki]: https://en.wikipedia.org/wiki/Checksum
-
+[github_new_repo]: https://github.com/new
diff --git a/learners/files/github.Rmd b/learners/files/github.Rmd
new file mode 100644
index 0000000..a33e5dc
--- /dev/null
+++ b/learners/files/github.Rmd
@@ -0,0 +1,67 @@
+## GitHub Requirements
+
+This part assumes you have a GitHub.com account.
+
+If you do not have a GitHub.com account you can create one [here][github_signup]
+
+The following steps will take you through the process of creating a SSH key pair to
+connect your terminal to GitHub. If you already have this set up, you may skip this part.
+
+
+:::::::::::::::::: callout
+
+
+### Opening files from the terminal
+
+Whenever you are required to open a file from the terminal, you may type `code /path/to/file`.
+
+This will also create the file if it does not yet exist.
+
+::::::::::::::::::
+
+
+### SSH Key
+
+After generating an account you will need to generate an SSH Key so that you can pull and push code from your terminal to GitHub.
+
+In your terminal run the following command
+
+```
+# Create the .ssh directory
+mkdir -p --mode 700 ~/.ssh
+
+ssh-keygen -f ~/.ssh/github -t ed25519 -q -N ""
+```
+
+### Add your public key to GitHub
+
+Head to [GitHub SSH and GPG keys][github_settings].
+
+Click `New SSH key`.
+set the title as the name of your computer (this can be anything), and under the 'Key',
+copy the contents of `~/.ssh/github.pub` from your terminal.
+
+### Setting your SSH Config
+
+Open up `~/.ssh/config` and add in the following code chunk:
+
+```
+Host github.com
+ IdentityFile /home/YOUR_USER_NAME/.ssh/github
+ User git
+```
+
+### Test your connection
+
+```
+ssh -T git@github.com
+```
+
+You should see a message like so
+
+```
+Hi alexiswl! You've successfully authenticated, but GitHub does not provide shell access.
+```
+
+[github_signup]: https://github.com/signup
+[github_settings]: https://github.com/settings/keys
diff --git a/learners/setup.Rmd b/learners/setup.Rmd
index 8f91c73..9a35bdb 100644
--- a/learners/setup.Rmd
+++ b/learners/setup.Rmd
@@ -128,6 +128,11 @@ dot - graphviz version 2.43.0 (0)
```
+
+```{r, child = 'files/github.Rmd'}
+
+```
+
```{r, child = 'files/data_setup.Rmd'}
```