Render bookdown

docs/01-intro.md

@@ -43,4 +43,4 @@ Examples and walkthroughs of common tasks on the AnVIL platform:
 
 Note that some sections of this book cover steps in a lot of detail. When navigating the table of contents, you can click subsection (e.g., 2.1, 4.3) headers a second time to expand the table of contents and enable the `scroll_highlight` feature. This can help you follow the separate steps within more clearly.
 
-<img src="01-intro_files/figure-html//1kGxHkP0JVPNF1kla5XEqaIt1yz9s4ZbgzJ2zfL7GmTE_gde0d2ef5f6_0_1.png" title="Double-clicking on the H2 headers (for example, 2.1) will expand the contents for view using the 'scroll_highlight' feature." alt="Double-clicking on the H2 headers (for example, 2.1) will expand the contents for view using the 'scroll_highlight' feature." width="480" />
+<img src="01-intro_files/figure-html//1kGxHkP0JVPNF1kla5XEqaIt1yz9s4ZbgzJ2zfL7GmTE_gde0d2ef5f6_0_1.png" alt="Double-clicking on the H2 headers (for example, 2.1) will expand the contents for view using the 'scroll_highlight' feature." width="480" />

docs/03-data-analysts.md

@@ -12,13 +12,13 @@ This chapter is targeted towards people who are joining an existing team on AnVI
 
 ### Goals for This Guide
 
-<img src="03-data-analysts_files/figure-html//1LT4wxVioJWtSpf3GV81hrbG8W2M-YWOaY7PmJObRioM_gd5c49c5c55_0_165.png" title="List of goals for this guide: 1) get your accounts and 2) link external accounts." alt="List of goals for this guide: 1) get your accounts and 2) link external accounts." width="480" />
+<img src="03-data-analysts_files/figure-html//1LT4wxVioJWtSpf3GV81hrbG8W2M-YWOaY7PmJObRioM_gd5c49c5c55_0_165.png" alt="List of goals for this guide: 1) get your accounts and 2) link external accounts." width="480" />
 
 ### Starting Setup
 
 **Terra** is the compute engine of AnVIL; i.e. where you will run your analyses.  Terra currently offers access to **Jupyter Notebooks** and **RStudio** for interactive analysis, as well as the **Workflow Description Language** (WDL) for batch processing of many samples.  Behind the scenes, Terra runs on Google Cloud Platform, so you will need a (free) Google Account.
 
-<img src="03-data-analysts_files/figure-html//1LT4wxVioJWtSpf3GV81hrbG8W2M-YWOaY7PmJObRioM_gd84a304855_0_138.png" title="Diagram illustrating the relationship between Terra and Google Cloud Platform." alt="Diagram illustrating the relationship between Terra and Google Cloud Platform." width="480" />
+<img src="03-data-analysts_files/figure-html//1LT4wxVioJWtSpf3GV81hrbG8W2M-YWOaY7PmJObRioM_gd84a304855_0_138.png" alt="Diagram illustrating the relationship between Terra and Google Cloud Platform." width="480" />
 
 In this guide, you will go through the following steps:
 
@@ -44,7 +44,7 @@ If you would like to create a Google account that is associated with your non-Gm
 
 You can always access Terra by going to [`anvil.terra.bio`](https://anvil.terra.bio/), or by clicking the link on the AnVIL home page.
 
-<img src="03-data-analysts_files/figure-html//1LT4wxVioJWtSpf3GV81hrbG8W2M-YWOaY7PmJObRioM_gde7783227e_0_31.png" title="Screenshot of the AnVIL home page. The button to &quot;launch Terra&quot; is highlighted." alt="Screenshot of the AnVIL home page. The button to &quot;launch Terra&quot; is highlighted." width="480" />
+<img src="03-data-analysts_files/figure-html//1LT4wxVioJWtSpf3GV81hrbG8W2M-YWOaY7PmJObRioM_gde7783227e_0_31.png" alt="Screenshot of the AnVIL home page. The button to &quot;launch Terra&quot; is highlighted." width="480" />
 
 ## Step 3: Link External Accounts (optional)
 

docs/04-consortia.md

@@ -19,7 +19,7 @@ table of contents and enable the `scroll_highlight` feature
 
 ### Goals for This Guide
 
-<img src="04-consortia_files/figure-html//1H6LfwdDpYxlZ_BhaRKIZnvqr_V_NxE2MfrZuXva8m-8_gd5c49c5c55_0_165.png" title="List of goals for this guide: 1) Choose your consortium role, 2) Get your accounts, and 3) Link external accounts." alt="List of goals for this guide: 1) Choose your consortium role, 2) Get your accounts, and 3) Link external accounts." width="480" />
+<img src="04-consortia_files/figure-html//1H6LfwdDpYxlZ_BhaRKIZnvqr_V_NxE2MfrZuXva8m-8_gd5c49c5c55_0_165.png" alt="List of goals for this guide: 1) Choose your consortium role, 2) Get your accounts, and 3) Link external accounts." width="480" />
 
 ### Choosing a Role
 

docs/06-tools-galaxy.md

@@ -7,7 +7,7 @@ One of the analysis platforms available on AnVIL is Galaxy. This platform offers
 
 Here is a video tutorial that describes the basics of using Galaxy on AnVIL.
 
-<iframe src="https://drive.google.com/file/d/16QEY8x-gBsUkKEeO3w_H-I4SLIBPloXd/preview" width="640" height="360" allow="autoplay"></iframe>
+<iframe width="560" height="315" src="https://youtu.be/9TEVu7QobOo?si=tLFXNe951vVJV4iN" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
 ### Objectives
 
@@ -17,7 +17,7 @@ Here is a video tutorial that describes the basics of using Galaxy on AnVIL.
 
 ### Slides
 
-The slides for this tutorial are are located [here](https://docs.google.com/presentation/d/1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q).
+The slides for this tutorial are are located [here](https://docs.google.com/presentation/d/1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q/edit?usp=sharing).
 
 ## Galaxy: Step-by-step guide
 
@@ -29,9 +29,17 @@ This step-by-step guide provides written instructions and screenshots for gettin
 
 Note that, in order to use Galaxy, you must have access to a Terra Workspace with permission to compute (i.e. you must be a "Writer" or "Owner" of the Workspace).
 
-Open your Workspace, and click on the “NOTEBOOKS” tab. Next, click on “Create a Cloud Environment for Galaxy”. You should see a popup window on the right side of the screen. Click on “NEXT” and “CREATE” to keep all settings as-is. This will take 8-10 minutes. When it is done, click “LAUNCH GALAXY”.
+Open your Workspace, and click on the “Environment configuration” button, a cloud icon on the righthand side of the screen. 
 
-<img src="06-tools-galaxy_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_ged15532ded_0_788.png" title="Screenshot of the Workspace Notebooks tab. The notebook tab name and the plus button that starts a cloud environment for Galaxy have been highlighted," 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," width="480" />
+<img src="06-tools-galaxy_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge20e585f11_0_9.png" alt="Screenshot of the Workspace that points to the Environment configuration button, an icon of a cloud with a lightning bolt." width="480" />
+
+Under Galaxy, click on “Create new Environment”. Click on “Next” and “Create” to keep all settings as-is. This will take 8-10 minutes.
+
+<img src="06-tools-galaxy_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge1182914a6_0_36.png" alt="The button that starts a cloud environment for Galaxy has been highlighted," width="480" />
+
+Click on "Open Galaxy" when the environment is ready.
+
+<img src="06-tools-galaxy_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge1182914a6_0_57.png" alt="The Open Galaxy button is highlighted in the ready environment popup." width="480" />
 
 ### Navigating Galaxy
 
@@ -44,7 +52,7 @@ Notice the three main sections.
 
 **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.
 
-<img src="06-tools-galaxy_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_ged15532ded_0_816.png" title="Screenshot of the Galaxy landing page. The Tools and History headings have been highlighted." alt="Screenshot of the Galaxy landing page. The Tools and History headings have been highlighted." width="480" />
+<img src="06-tools-galaxy_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_ged15532ded_0_816.png" alt="Screenshot of the Galaxy landing page. The Tools and History headings have been highlighted." width="480" />
 
 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.
 
@@ -53,14 +61,14 @@ On the welcome page, there are links to tutorials. You may try these out on your
 
 Once you are done with your activity, you’ll need to shut down your Galaxy cloud environment. This frees up the cloud resources for others and minimizes computing cost. The following steps will delete your work, so make sure you are completely finished at this point. Otherwise, you will have to repeat your work from the previous steps.
 
-Return to AnVIL, and find the Galaxy logo that shows your cloud environment is running. Click on this logo:
+Return to AnVIL, and find the Galaxy logo that shows your cloud environment is running. Click on this logo.
 
-<img src="06-tools-galaxy_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_134.png" title="Screenshot of the Workspace menu. The currently running Galaxy cloud environment logo on the top right of the page is highlighted." alt="Screenshot of the Workspace menu. The currently running Galaxy cloud environment logo on the top right of the page is highlighted." width="480" />
+<img src="06-tools-galaxy_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge20e585f11_0_248.png" alt="Screenshot of the Workspace menu. The currently running Galaxy cloud environment logo on the right sidebar is highlighted." width="480" />
 
-Next, click on “DELETE ENVIRONMENT OPTIONS”:
+Next, click on "Settings". Click on "Delete Environment".
 
-<img src="06-tools-galaxy_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_140.png" title="Screenshot of the cloud environment pop out menu. The “DELETE ENVIRONMENT OPTIONS” link is highlighted." alt="Screenshot of the cloud environment pop out menu. The “DELETE ENVIRONMENT OPTIONS” link is highlighted." width="480" />
+<img src="06-tools-galaxy_files/figure-html//1yYCg4cPVBMMDghT17B4XzROieqyMH99Ex9nMm_Scm9Q_ge20e585f11_0_256.png" alt="Screenshot of the cloud environment pop out menu. The &quot;Delete Environment&quot; button is highlighted." width="480" />
 
-Finally, select “Delete everything, including persistent disk”. Make sure you are done with the activity and then click “DELETE”.
+Finally, select "Delete everything, including persistent disk". Make sure you are done with the activity and then click "Delete".
 
-<img src="06-tools-galaxy_files/figure-html//182AOzMaiyrreinnsRX2VhH7YsVgvAp4xtIB_7Mzmk6I_gf243efded1_0_146.png" title="Screenshot of the cloud environment pop out menu. The “Delete everything, including persistent disk” radio button has been checked and is highlighted. The “DELETE” button is highlighted." alt="Screenshot of the cloud environment pop out menu. The “Delete everything, including persistent disk” radio button has been checked and is highlighted. The “DELETE” button is highlighted." width="480" />
+<img src="06-tools-galaxy_files/figure-html//1UIfBMQcujMzyNTyIiMXQ6eU0DdWHmI9QUtseGylg6Ms_g117989bd49c_0_0.png" alt="Screenshot of the cloud environment pop out menu. The “Delete everything, including persistent disk” radio button has been checked and is highlighted. The “Delete” button is highlighted." width="480" />