diff --git a/docs/index.md b/docs/index.md
index a2e81df..cb41a29 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -14,7 +14,7 @@ Log onto O2 via the command line and check two things (first-time only):
* Remove any path you load using the R env variables that could be in your `.Rprofile` or `.bashrc`
Go to the [O2 Portal](https://o2portal.rc.hms.harvard.edu/) and select `HMS-RC Application`, then `RStudio Environment`
-
+
Start Rstudio with using your desired partition, memory, core and time directives. Add these modules to "Modules to be loaded":
```
@@ -22,11 +22,11 @@ Start Rstudio with using your desired partition, memory, core and time directive
```
Click "Launch"
-
+
Open RStudio by clicking on the "Connect to RStudio Server"
-
+
When the session is started, set your library path by typing this command in your console Rstudio window in order to be able to load `bcbioR`:
@@ -48,7 +48,7 @@ packageVersion("bcbioR")
Make sure the version is **0.4.*** or later.
-
+
> Note: If you are working in your local environment, install `bcbioR` with
> ```
@@ -126,7 +126,9 @@ Next, we need to set the library that `bcbioR` will use each time you open up th
Now, we will use `bcbioR` to set-up the directory structure that we will be using for our analysis using the following command:
```
-bcbioR::bcbio_templates(type="base", outpath=".", org="hcbc")
+bcbioR::bcbio_templates(type="base", outpath=".", org="
+
+")
```
### Setting up GitHub and RStudio
@@ -173,7 +175,7 @@ Note: In order to see hidden file in your file browser on the O2 Portal, you wil
Now, we would like to get the Git tab into our Workspace Browser (where `Environment`, `History`, `Connections` and `Tutorial` tabs are located). We show this transition below:
-
+
In order to do this we will use the following command:
@@ -232,7 +234,7 @@ Now, we are going to create our first commit. In order to do this, we need to:
These steps are summarized in the GIF below:
-
+
#### Pushing our initial commit
@@ -255,10 +257,10 @@ If you do not have a valid GitHub token, this will give you an error (see [below
If the push is successful, then it will look like this GIF below:
-
+
> Note: You might get a GitHub 404 error page (see image below) when you do your first push to GitHub. Just refresh the page in your browser and it should be resolve itself.
-> 
+> 
##### Expired or non-existent GitHub token
@@ -287,13 +289,13 @@ Then you can provide the following line of code to store your GitHub token for f
git config --global credential.helper store
This process is summarized in the GIF below:
-
+
Now that we have let Git know to store our GitHub token, we can create one. In order to create a GitHub token, you will need to run:
usethis::create_github_token()
This will take you to a GitHub Webpage. It may prompt you to sign-in to GitHub. From here, you need to name your token and select an expiration date for your token. Then, scroll to the bottom of the page and left-click Generate token. These step are summarized in the GIF below:
-
+
Next, you will want to copy your GitHub Token and go back to RStudio. We need to set our credentials by using the command:
gitcreds::gitcreds_set()
@@ -305,7 +307,7 @@ Paste in your copied GitHub token and hit Return/Enter. It should ret
-> Done.
These steps are summarized in the GIF below:
-
+
Now you should have a hidden file called .git-credentials in your Home directory and it should look like:
https://PersonalAccessToken:YOUR_GITHUB_TOKEN@github.com
@@ -340,7 +342,7 @@ We are going to edit the `README.MD` using these steps:
These steps are summarized in the GIF below:
-
+
### Pushing the edit to GitHub
@@ -354,7 +356,7 @@ Now that we have made this commit, we will push it to GitHub using these steps:
You should now see the HBC code as the header to the `README.md` on GitHub. These steps are summarized in the GIF below:
-
+
## Using the template reports
diff --git a/docs/img/GitHub_404_error_with_label.png b/overrides/img/GitHub_404_error_with_label.png
similarity index 100%
rename from docs/img/GitHub_404_error_with_label.png
rename to overrides/img/GitHub_404_error_with_label.png
diff --git a/docs/img/GitHub_initial_push.gif b/overrides/img/GitHub_initial_push.gif
similarity index 100%
rename from docs/img/GitHub_initial_push.gif
rename to overrides/img/GitHub_initial_push.gif
diff --git a/docs/img/GitHub_token_Part_1.gif b/overrides/img/GitHub_token_Part_1.gif
similarity index 100%
rename from docs/img/GitHub_token_Part_1.gif
rename to overrides/img/GitHub_token_Part_1.gif
diff --git a/docs/img/GitHub_token_Part_2.gif b/overrides/img/GitHub_token_Part_2.gif
similarity index 100%
rename from docs/img/GitHub_token_Part_2.gif
rename to overrides/img/GitHub_token_Part_2.gif
diff --git a/docs/img/Git_config.gif b/overrides/img/Git_config.gif
similarity index 100%
rename from docs/img/Git_config.gif
rename to overrides/img/Git_config.gif
diff --git a/docs/img/Git_pane_RStudio.png b/overrides/img/Git_pane_RStudio.png
similarity index 100%
rename from docs/img/Git_pane_RStudio.png
rename to overrides/img/Git_pane_RStudio.png
diff --git a/docs/img/Git_token_Part_1.gif b/overrides/img/Git_token_Part_1.gif
similarity index 100%
rename from docs/img/Git_token_Part_1.gif
rename to overrides/img/Git_token_Part_1.gif
diff --git a/docs/img/Git_token_Part_2.gif b/overrides/img/Git_token_Part_2.gif
similarity index 100%
rename from docs/img/Git_token_Part_2.gif
rename to overrides/img/Git_token_Part_2.gif
diff --git a/docs/img/Guideline_commit_push.gif b/overrides/img/Guideline_commit_push.gif
similarity index 100%
rename from docs/img/Guideline_commit_push.gif
rename to overrides/img/Guideline_commit_push.gif
diff --git a/docs/img/Guideline_push.gif b/overrides/img/Guideline_push.gif
similarity index 100%
rename from docs/img/Guideline_push.gif
rename to overrides/img/Guideline_push.gif
diff --git a/docs/img/Initial_commit.gif b/overrides/img/Initial_commit.gif
similarity index 100%
rename from docs/img/Initial_commit.gif
rename to overrides/img/Initial_commit.gif
diff --git a/docs/img/O2_connect_to_RStudio_with_label.png b/overrides/img/O2_connect_to_RStudio_with_label.png
similarity index 100%
rename from docs/img/O2_connect_to_RStudio_with_label.png
rename to overrides/img/O2_connect_to_RStudio_with_label.png
diff --git a/docs/img/O2_portal_page_with_label.png b/overrides/img/O2_portal_page_with_label.png
similarity index 100%
rename from docs/img/O2_portal_page_with_label.png
rename to overrides/img/O2_portal_page_with_label.png
diff --git a/docs/img/O2_portal_request.gif b/overrides/img/O2_portal_request.gif
similarity index 100%
rename from docs/img/O2_portal_request.gif
rename to overrides/img/O2_portal_request.gif
diff --git a/docs/img/Version_check_bcbioR.gif b/overrides/img/Version_check_bcbioR.gif
similarity index 100%
rename from docs/img/Version_check_bcbioR.gif
rename to overrides/img/Version_check_bcbioR.gif