Elizabeth/Create student anvil guide

04-billing_modules.Rmd

@@ -1,7 +1,7 @@
 ```{r echo = FALSE}
 knitr::opts_chunk$set(out.width = "100%")
 ```
-# (PART\*) Using AnVIL {-}
+# (PART\*) AnVIL Overview {-}
 
 # Billing
 

07-instructor-guide.Rmd → 07-instructor_guide.Rmd

@@ -1,4 +1,4 @@
-# (PART\*) Instructor Guide {-}
+# (PART\*) Instructor Guide to AnVIL {-}
 
 # Notes for Instructors 
 

08-student_anvil_guide.Rmd

@@ -0,0 +1,149 @@
+# (PART\*) Student Guide to AnVIL {-}
+
+
+```{r, include = FALSE}
+ottrpal::set_knitr_image_path()
+```
+
+# Using RStudio on AnVIL
+
+In the next few steps, you will walk through how to get set up to use RStudio on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment.
+
+Use a web browser to go to the AnVIL website. In the browser type:
+
+```
+anvil.terra.bio
+```
+
+:::{.notice}
+**Tip**
+At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other.
+:::
+
+Your instructor will give you information on which workspace you should clone.
+
+## Video overview of RStudio on AnVIL
+
+```{r, echo = FALSE, results='asis'}
+cow::borrow_chapter(
+  doc_path = "child/_child_rstudio_video.Rmd",
+  repo_name = "jhudsl/AnVIL_Template"
+)
+```
+
+## Launching RStudio
+
+```{r, echo = FALSE, results='asis'}
+cow::borrow_chapter(
+  doc_path = "child/_child_rstudio_launch.Rmd",
+  repo_name = "jhudsl/AnVIL_Template"
+)
+```
+
+## Touring RStudio
+
+```{r, echo = FALSE, results='asis'}
+cow::borrow_chapter(
+  doc_path = "child/_child_rstudio_tour.Rmd",
+  repo_name = "jhudsl/AnVIL_Template"
+)
+```
+
+## Pausing RStudio
+
+```{r, echo = FALSE, results='asis'}
+cow::borrow_chapter(
+  doc_path = "child/_child_rstudio_pause.Rmd",
+  repo_name = "jhudsl/AnVIL_Template"
+)
+```
+
+
+# Using Galaxy on AnVIL
+
+In the next few steps, you will walk through how to get set up to use Galaxy on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment.
+
+Use a web browser to go to the AnVIL website. In the browser type:
+
+```
+anvil.terra.bio
+```
+
+:::{.notice}
+**Tip**
+At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other.
+:::
+
+Your instructor will give you information on which workspace you should clone. After logging in, click “View Workspaces”. Select the “Public” tab.  In the top search bar type the activity workspace. 
+
+Clone the workspace by clicking the teardrop button (![teardrop button](resources/images/teardrop.png){#id .class width=25 height=20px}). And selecting “Clone”.
+
+```{r, echo=FALSE, fig.alt='Screenshot showing the teardrop button. The button has been clicked revealing the "clone" option. The Clone option and the teardrop button are highlighted.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_625")
+```
+
+In the first box, give your Workspace clone a name by adding an underscore (“_”) and your name. For example, “SARS-CoV-2-Genome_Ava_Hoffman”. Next, select the Billing project provided by your instructor. Leave the bottom two boxes as-is and click “CLONE WORKSPACE”.
+
+```{r, echo=FALSE, fig.alt='Screenshot showing the "clone a workspace" popout. The Workspace name, Billing Project, and Clone Workspace button have been filled in and highlighted.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_648")
+```
+
+## Starting Galaxy {#starting-galaxy}
+
+Galaxy is a free, relatively easy to use bioinformatics implementation package. It changes command line programs into GUI based programs and is a great tool for performing bioinformatics analysis without having to update software or worry too much about coding. In order to use Galaxy, we need to create a cloud environment. This is like quickly renting a few computers from Google as the engine to power our Galaxy analysis. 
+
+:::{.warning}
+Currently, you will need to use Chrome or Safari as your browser for Galaxy cloud environments to work.
+:::
+
+In your new Workspace, click on the “ANALYSES” tab. Next, click on “START”. You should see a popup window on the right side of the screen. Click on the Galaxy logo to proceed.
+
+```{r, echo=FALSE, fig.alt='Screenshot of the Workspace Notebooks tab. The notebook tab name and the plus button that starts a cloud environment for Galaxy have been highlighted,'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_788")
+```
+
+Click on “NEXT” and “CREATE” to keep all settings as-is.
+
+```{r, echo=FALSE, fig.alt='The CREATE button among cloud environments has been highlighted.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_798")
+```
+
+Click on the Galaxy icon. 
+
+```{r, echo=FALSE, fig.alt='The Galaxy icon appears if the environment has been successfully launched.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.g2283b458fae_100_31")
+```
+
+You will see that the environment is still being set up.
+
+```{r, echo=FALSE, fig.alt='The status of the cloud computing environment shows that it is still being set up.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.g2283b458fae_100_38")
+```
+
+This will take 8-10 minutes. When it is done, click “Open”. You might need to refresh the page.
+
+```{r, echo=FALSE, fig.alt='The Provisioning status text has changed to "Launch Galaxy" indicating the cloud environment is ready to use.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.g2283b458fae_100_46")
+```
+
+:::{.notice}
+Remember that you can refresh your browser or navigate away at any time. This is because the connection to the environment is in the cloud, not on your personal computer.
+:::
+
+You can also follow along with the first ~2 minutes of [this video](https://jhudatascience.org/AnVIL_Book_Getting_Started/starting-galaxy.html) to start Galaxy on AnVIL.
+
+## Navigating Galaxy
+
+Notice the three main sections.
+
+**Tools** - These are all of the bioinformatics tool packages available for you to use.
+
+**The Main Dashboard** - This contains flash messages and posts when you first open Galaxy, but when we are using data this is the main interface area.
+
+**History** - When you start a project you will be able to see all of the documents in the project in the history. Now be aware, this can become very busy. Also the naming that Galaxy uses is not very intuitive, so you must make sure that you label your files with something that makes sense to you.
+
+```{r, echo=FALSE, fig.alt='Screenshot of the Galaxy landing page. The Tools and History headings have been highlighted.'}
+ottrpal::include_slide("https://docs.google.com/presentation/d/182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I/edit#slide=id.ged15532ded_0_816")
+```
+
+On the welcome page, there are links to tutorials. You may try these out on your own. If you want to try a new analysis this is a good place to start.

08-data_exploration.Rmd → 09-data_exploration.Rmd

@@ -22,65 +22,11 @@ cow::borrow_chapter(
 
 This activity will teach you how to use the AnVIL platform to:
 
-1. Get started working on AnVIL
-1. Launch RStudio
 1. Import data into RStudio
-1. Examine csv file that contains the soil testing data from the BioDIGS project
+1. Examine a csv file that contains the soil testing data from the BioDIGS project
 1. Calculate summary statistics for variables in the soil testing data
-1. Create and interpret histograms and boxplots for variables in the soil testing data.
+1. Create and interpret histograms and boxplots for variables in the soil testing data
 
-## Getting Started
-
-In the next few steps, you will walk through how to get set up to use RStudio on the AnVIL platform. AnVIL is centered around different “Workspaces”. Each Workspace functions almost like a mini code laboratory - it is a place where data can be examined, stored, and analyzed. The first thing we want to do is to copy or “clone” a Workspace to create a space for you to experiment.
-
-Use a web browser to go to the AnVIL website. In the browser type:
-
-```
-anvil.terra.bio
-```
-
-:::{.notice}
-**Tip**
-At this point, it might make things easier to open up a new window in your browser and split your screen. That way, you can follow along with this guide on one side and execute the steps on the other.
-:::
-
-Your instructor will give you information on which workspace you should clone.
-
-### Video overview of RStudio on AnVIL
-
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_rstudio_video.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
-
-### Launching RStudio
-
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_rstudio_launch.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
-
-### Touring RStudio
-
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_rstudio_tour.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
-
-### Pausing RStudio
-
-```{r, echo = FALSE, results='asis'}
-cow::borrow_chapter(
-  doc_path = "child/_child_rstudio_pause.Rmd",
-  repo_name = "jhudsl/AnVIL_Template"
-)
-```
 
 ## Part 1. Data Import
 

_bookdown.yml

@@ -8,8 +8,9 @@ rmd_files: ["index.Rmd",
             "04-billing_modules.Rmd",
             "05-anvil_onboarding.Rmd",
             "06-using_platforms_modules.Rmd",
-            "07-instructor-guide.Rmd",
-            "08-data_exploration.Rmd",
+            "07-instructor_guide.Rmd",
+            "08-student_anvil_guide.Rmd",
+            "09-data_exploration.Rmd",
             "About.Rmd",
             "References.Rmd"]
 new_session: yes