Render bookdown

docs/06-using_galaxy.md

@@ -1,6 +1,6 @@
 
 
-# Programming Platforms
+# Using Galaxy
 
 This section provide a general overview of how to use Galaxy on AnVIL.
 

docs/08-student_guide.md

@@ -2,6 +2,8 @@
 
 
 
+# AMR Resistance with Galaxy
+
 ## AnVIL Account Setup
 
 :::: {.borrowed_chunk}
@@ -79,3 +81,5 @@ To clone an AnVIL Workspace:
 
 1. The new Workspace should now show up under https://anvil.terra.bio/#workspaces. This is your own copy of the Workspace to work in.
 ::::
+
+More details coming soon!

docs/404.html

@@ -146,63 +146,64 @@
 <li class="chapter" data-level="6.1" data-path="anvil-workspace.html"><a href="anvil-workspace.html#create-google-account"><i class="fa fa-check"></i><b>6.1</b> Create Google Account</a></li>
 <li class="chapter" data-level="6.2" data-path="anvil-workspace.html"><a href="anvil-workspace.html#clone-the-workspace"><i class="fa fa-check"></i><b>6.2</b> Clone the Workspace</a></li>
 </ul></li>
-<li class="chapter" data-level="7" data-path="programming-platforms.html"><a href="programming-platforms.html"><i class="fa fa-check"></i><b>7</b> Programming Platforms</a>
+<li class="chapter" data-level="7" data-path="using-galaxy.html"><a href="using-galaxy.html"><i class="fa fa-check"></i><b>7</b> Using Galaxy</a>
 <ul>
-<li class="chapter" data-level="7.1" data-path="programming-platforms.html"><a href="programming-platforms.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Galaxy</a>
+<li class="chapter" data-level="7.1" data-path="using-galaxy.html"><a href="using-galaxy.html#video-overview-on-using-galaxy"><i class="fa fa-check"></i><b>7.1</b> Video overview on using Galaxy</a>
 <ul>
-<li class="chapter" data-level="7.1.1" data-path="programming-platforms.html"><a href="programming-platforms.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
-<li class="chapter" data-level="7.1.2" data-path="programming-platforms.html"><a href="programming-platforms.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
+<li class="chapter" data-level="7.1.1" data-path="using-galaxy.html"><a href="using-galaxy.html#objectives"><i class="fa fa-check"></i><b>7.1.1</b> Objectives</a></li>
+<li class="chapter" data-level="7.1.2" data-path="using-galaxy.html"><a href="using-galaxy.html#slides"><i class="fa fa-check"></i><b>7.1.2</b> Slides</a></li>
 </ul></li>
-<li class="chapter" data-level="7.2" data-path="programming-platforms.html"><a href="programming-platforms.html#starting-galaxy"><i class="fa fa-check"></i><b>7.2</b> Starting Galaxy</a></li>
-<li class="chapter" data-level="7.3" data-path="programming-platforms.html"><a href="programming-platforms.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.3</b> Navigating Galaxy</a></li>
-<li class="chapter" data-level="7.4" data-path="programming-platforms.html"><a href="programming-platforms.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Deleting Galaxy</a></li>
+<li class="chapter" data-level="7.2" data-path="using-galaxy.html"><a href="using-galaxy.html#starting-galaxy"><i class="fa fa-check"></i><b>7.2</b> Starting Galaxy</a></li>
+<li class="chapter" data-level="7.3" data-path="using-galaxy.html"><a href="using-galaxy.html#navigating-galaxy"><i class="fa fa-check"></i><b>7.3</b> Navigating Galaxy</a></li>
+<li class="chapter" data-level="7.4" data-path="using-galaxy.html"><a href="using-galaxy.html#deleting-galaxy"><i class="fa fa-check"></i><b>7.4</b> Deleting Galaxy</a></li>
 </ul></li>
-<li class="chapter" data-level="" data-path=""><a href="#part-student-activity"><i class="fa fa-check"></i>(PART*) Student Activity</a>
+<li class="part"><span><b>Student Activity</b></span></li>
+<li class="chapter" data-level="8" data-path="amr-resistance-with-galaxy.html"><a href="amr-resistance-with-galaxy.html"><i class="fa fa-check"></i><b>8</b> AMR Resistance with Galaxy</a>
 <ul>
-<li class="chapter" data-level="7.5" data-path=""><a href="#anvil-account-setup"><i class="fa fa-check"></i><b>7.5</b> AnVIL Account Setup</a></li>
-<li class="chapter" data-level="7.6" data-path="programming-platforms.html"><a href="programming-platforms.html#cloning-the-anvil-workspace"><i class="fa fa-check"></i><b>7.6</b> Cloning the AnVIL Workspace</a></li>
+<li class="chapter" data-level="8.1" data-path="amr-resistance-with-galaxy.html"><a href="amr-resistance-with-galaxy.html#anvil-account-setup"><i class="fa fa-check"></i><b>8.1</b> AnVIL Account Setup</a></li>
+<li class="chapter" data-level="8.2" data-path="amr-resistance-with-galaxy.html"><a href="amr-resistance-with-galaxy.html#cloning-the-anvil-workspace"><i class="fa fa-check"></i><b>8.2</b> Cloning the AnVIL Workspace</a></li>
 </ul></li>
 <li class="part"><span><b>Instructor Checklist for AnVIL</b></span></li>
-<li class="chapter" data-level="8" data-path="notes-for-instructors.html"><a href="notes-for-instructors.html"><i class="fa fa-check"></i><b>8</b> Notes for Instructors</a></li>
-<li class="chapter" data-level="9" data-path="checklist-for-running-activities-on-anvil.html"><a href="checklist-for-running-activities-on-anvil.html"><i class="fa fa-check"></i><b>9</b> Checklist for Running Activities on AnVIL</a>
+<li class="chapter" data-level="9" data-path="notes-for-instructors.html"><a href="notes-for-instructors.html"><i class="fa fa-check"></i><b>9</b> Notes for Instructors</a></li>
+<li class="chapter" data-level="10" data-path="checklist-for-running-activities-on-anvil.html"><a href="checklist-for-running-activities-on-anvil.html"><i class="fa fa-check"></i><b>10</b> Checklist for Running Activities on AnVIL</a>
 <ul>
 <li class="chapter" data-level="" data-path="checklist-for-running-activities-on-anvil.html"><a href="checklist-for-running-activities-on-anvil.html#before-the-class-begins"><i class="fa fa-check"></i>Before the class begins</a></li>
 <li class="chapter" data-level="" data-path="checklist-for-running-activities-on-anvil.html"><a href="checklist-for-running-activities-on-anvil.html#after-the-class-ends"><i class="fa fa-check"></i>After the class ends</a></li>
 </ul></li>
-<li class="chapter" data-level="10" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html"><i class="fa fa-check"></i><b>10</b> Setting up Billing on AnVIL</a>
+<li class="chapter" data-level="11" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html"><i class="fa fa-check"></i><b>11</b> Setting up Billing on AnVIL</a>
 <ul>
-<li class="chapter" data-level="10.1" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#billing-project"><i class="fa fa-check"></i><b>10.1</b> Creating a billing project</a></li>
-<li class="chapter" data-level="10.2" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#adding-instructors-as-owner"><i class="fa fa-check"></i><b>10.2</b> Adding Instructors as “Owner”</a></li>
-<li class="chapter" data-level="10.3" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#adding-students-as-user"><i class="fa fa-check"></i><b>10.3</b> Adding Students as “User”</a></li>
-<li class="chapter" data-level="10.4" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#understanding-the-various-billing-costs"><i class="fa fa-check"></i><b>10.4</b> Understanding the various billing costs</a></li>
-<li class="chapter" data-level="10.5" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#estimating-costs-before-the-class-begins"><i class="fa fa-check"></i><b>10.5</b> Estimating costs before the class begins</a></li>
-<li class="chapter" data-level="10.6" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#how-much-does-a-class-cost"><i class="fa fa-check"></i><b>10.6</b> How much does a class cost?</a></li>
+<li class="chapter" data-level="11.1" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#billing-project"><i class="fa fa-check"></i><b>11.1</b> Creating a billing project</a></li>
+<li class="chapter" data-level="11.2" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#adding-instructors-as-owner"><i class="fa fa-check"></i><b>11.2</b> Adding Instructors as “Owner”</a></li>
+<li class="chapter" data-level="11.3" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#adding-students-as-user"><i class="fa fa-check"></i><b>11.3</b> Adding Students as “User”</a></li>
+<li class="chapter" data-level="11.4" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#understanding-the-various-billing-costs"><i class="fa fa-check"></i><b>11.4</b> Understanding the various billing costs</a></li>
+<li class="chapter" data-level="11.5" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#estimating-costs-before-the-class-begins"><i class="fa fa-check"></i><b>11.5</b> Estimating costs before the class begins</a></li>
+<li class="chapter" data-level="11.6" data-path="setting-up-billing-on-anvil.html"><a href="setting-up-billing-on-anvil.html#how-much-does-a-class-cost"><i class="fa fa-check"></i><b>11.6</b> How much does a class cost?</a></li>
 </ul></li>
-<li class="chapter" data-level="11" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html"><i class="fa fa-check"></i><b>11</b> Setting up the Class Activity</a>
+<li class="chapter" data-level="12" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html"><i class="fa fa-check"></i><b>12</b> Setting up the Class Activity</a>
 <ul>
-<li class="chapter" data-level="11.1" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#overview-of-class-setup"><i class="fa fa-check"></i><b>11.1</b> Overview of Class Setup</a></li>
-<li class="chapter" data-level="11.2" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#collect-google-ids"><i class="fa fa-check"></i><b>11.2</b> Collect Google IDs</a></li>
-<li class="chapter" data-level="11.3" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#set-up-groups"><i class="fa fa-check"></i><b>11.3</b> Set Up Groups</a>
+<li class="chapter" data-level="12.1" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#overview-of-class-setup"><i class="fa fa-check"></i><b>12.1</b> Overview of Class Setup</a></li>
+<li class="chapter" data-level="12.2" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#collect-google-ids"><i class="fa fa-check"></i><b>12.2</b> Collect Google IDs</a></li>
+<li class="chapter" data-level="12.3" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#set-up-groups"><i class="fa fa-check"></i><b>12.3</b> Set Up Groups</a>
 <ul>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#instructor-group-instructor-group"><i class="fa fa-check"></i>Instructor Group {#instructor-group}</a></li>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#student-group-student-group"><i class="fa fa-check"></i>Student Group {#student-group}</a></li>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#group-email-lists"><i class="fa fa-check"></i>Group Email Lists</a></li>
 </ul></li>
-<li class="chapter" data-level="11.4" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#set-up-billing-projects"><i class="fa fa-check"></i><b>11.4</b> Set Up Billing Projects</a>
+<li class="chapter" data-level="12.4" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#set-up-billing-projects"><i class="fa fa-check"></i><b>12.4</b> Set Up Billing Projects</a>
 <ul>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#instructor-billing-project-instructor-billing-project"><i class="fa fa-check"></i>Instructor Billing Project {#instructor-billing-project}</a></li>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#student-billing-project-student-billing-project"><i class="fa fa-check"></i>Student Billing Project {#student-billing-project}</a></li>
 </ul></li>
-<li class="chapter" data-level="11.5" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#set-permissions-on-the-workspace"><i class="fa fa-check"></i><b>11.5</b> Set Permissions on the Workspace</a>
+<li class="chapter" data-level="12.5" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#set-permissions-on-the-workspace"><i class="fa fa-check"></i><b>12.5</b> Set Permissions on the Workspace</a>
 <ul>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#add-instructors-as-owner"><i class="fa fa-check"></i>Add Instructors as “Owner”</a></li>
 <li class="chapter" data-level="" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#add-students-as-reader"><i class="fa fa-check"></i>Add Students as “Reader”</a></li>
 </ul></li>
-<li class="chapter" data-level="11.6" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#notify-terra"><i class="fa fa-check"></i><b>11.6</b> Notify Terra</a></li>
+<li class="chapter" data-level="12.6" data-path="setting-up-the-class-activity.html"><a href="setting-up-the-class-activity.html#notify-terra"><i class="fa fa-check"></i><b>12.6</b> Notify Terra</a></li>
 </ul></li>
-<li class="chapter" data-level="12" data-path="getting-credit-for-professional-development.html"><a href="getting-credit-for-professional-development.html"><i class="fa fa-check"></i><b>12</b> Getting Credit for Professional Development</a></li>
+<li class="chapter" data-level="13" data-path="getting-credit-for-professional-development.html"><a href="getting-credit-for-professional-development.html"><i class="fa fa-check"></i><b>13</b> Getting Credit for Professional Development</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
-<li class="chapter" data-level="13" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>13</b> References</a></li>
+<li class="chapter" data-level="14" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>14</b> References</a></li>
 <li class="divider"></li>
 <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
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