From cad50d990527736b858620e192c2d061588de1ff Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 9 Jul 2024 00:03:29 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 1fd047eb00559d78db7f0e2e56238e0180f3bfd1
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-07-08 22:35:41 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : b6de3a9234049d930e40c3e2a85b16fc5bcf9512
Branch  : main
Author  : kerchner@gwu.edu <kerchner@gwu.edu>
Time    : 2024-07-08 22:34:58 +0000
Message : Clarified setup instructions
---
 404.html                         |  4 ++--
 AMI-setup.html                   |  6 +++---
 CODE_OF_CONDUCT.html             |  2 +-
 LICENSE.html                     |  2 +-
 faq.html                         |  2 +-
 index.html                       | 36 ++++++++++++++++----------------
 instructor-notes.html            |  4 ++--
 instructor/404.html              |  4 ++--
 instructor/AMI-setup.html        |  6 +++---
 instructor/CODE_OF_CONDUCT.html  |  2 +-
 instructor/LICENSE.html          |  2 +-
 instructor/faq.html              |  2 +-
 instructor/index.html            | 36 ++++++++++++++++----------------
 instructor/instructor-notes.html |  4 ++--
 instructor/profiles.html         |  4 ++--
 instructor/reference.html        |  2 +-
 instructor/teaching_demos.html   |  2 +-
 pkgdown.yml                      |  2 +-
 profiles.html                    |  4 ++--
 reference.html                   |  2 +-
 teaching_demos.html              |  2 +-
 21 files changed, 65 insertions(+), 65 deletions(-)

diff --git a/404.html b/404.html
index b2b1a7be..a6d1bf2d 100644
--- a/404.html
+++ b/404.html
@@ -273,8 +273,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/404.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/AMI-setup.html b/AMI-setup.html
index b8057ee4..c9557224 100644
--- a/AMI-setup.html
+++ b/AMI-setup.html
@@ -333,7 +333,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Connect to your Amazon Instance (MacOS/Linux)
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
 <li><p>You should see that you have one instance. To proceed, the
@@ -390,7 +390,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Connect to your Amazon instance (Windows)
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Download the PuTTY application at: <a href="https://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a></p></li>
 <li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
@@ -531,7 +531,7 @@ <h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#wa
   "identifier": "https://datacarpentry.github.io/genomics-workshop/AMI-setup.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 1df4666b..b71e44e5 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -300,7 +300,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 94277366..ac0853df 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -352,7 +352,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/LICENSE.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/faq.html b/faq.html
index 998de0b5..b8ec8e15 100644
--- a/faq.html
+++ b/faq.html
@@ -474,7 +474,7 @@ <h3 id="does-the-aws-image-location-matter-do-i-need-to-set-up-an-ami-in-a-diffe
   "identifier": "https://datacarpentry.github.io/genomics-workshop/faq.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2024-01-08",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 616a1d66..1c892f0c 100644
--- a/index.html
+++ b/index.html
@@ -400,7 +400,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ul><li>
 <strong>If you already have a spreadsheet program such as Microsoft
@@ -482,7 +482,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Mac OS X
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ul><li>
 <strong>If you already have a spreadsheet program such as Microsoft
@@ -506,7 +506,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <ul><li>
 <strong>If you already have a spreadsheet program such as Microsoft
@@ -628,7 +628,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -651,7 +651,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -677,7 +677,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -697,7 +697,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -743,7 +743,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -762,7 +762,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -801,7 +801,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -833,7 +833,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -852,7 +852,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -887,7 +887,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -922,7 +922,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -963,7 +963,7 @@ <h3 class="accordion-header" id="headingSpoiler15">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -982,7 +982,7 @@ <h3 class="accordion-header" id="headingSpoiler16">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -1066,8 +1066,8 @@ <h3 id="igv">IGV<a class="anchor" aria-label="anchor" href="#igv"></a></h3>
   "url": "https://datacarpentry.github.io/genomics-workshop/index.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/index.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 148b4c43..3e3a307d 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -300,8 +300,8 @@ <h4 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor-notes.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 1b3200c6..8a5033b5 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -267,8 +267,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/404.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/AMI-setup.html b/instructor/AMI-setup.html
index 73d67077..a4177d41 100644
--- a/instructor/AMI-setup.html
+++ b/instructor/AMI-setup.html
@@ -329,7 +329,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Connect to your Amazon Instance (MacOS/Linux)
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
 <li><p>You should see that you have one instance. To proceed, the
@@ -386,7 +386,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Connect to your Amazon instance (Windows)
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Download the PuTTY application at: <a href="https://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a></p></li>
 <li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
@@ -527,7 +527,7 @@ <h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#wa
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/AMI-setup.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index d1b245c3..01ca3b8e 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -296,7 +296,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index f3e09773..bd40813e 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -348,7 +348,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/LICENSE.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/faq.html b/instructor/faq.html
index fb97d76d..7ef81849 100644
--- a/instructor/faq.html
+++ b/instructor/faq.html
@@ -470,7 +470,7 @@ <h3 id="does-the-aws-image-location-matter-do-i-need-to-set-up-an-ami-in-a-diffe
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/faq.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2024-01-08",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index a5198ec5..eac5fb2f 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -399,7 +399,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ul><li>
 <strong>If you already have a spreadsheet program such as Microsoft
@@ -481,7 +481,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Mac OS X
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ul><li>
 <strong>If you already have a spreadsheet program such as Microsoft
@@ -505,7 +505,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <ul><li>
 <strong>If you already have a spreadsheet program such as Microsoft
@@ -627,7 +627,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -650,7 +650,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -676,7 +676,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -696,7 +696,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -742,7 +742,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -761,7 +761,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -800,7 +800,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -832,7 +832,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -851,7 +851,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -886,7 +886,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -921,7 +921,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -962,7 +962,7 @@ <h3 class="accordion-header" id="headingSpoiler15">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -981,7 +981,7 @@ <h3 class="accordion-header" id="headingSpoiler16">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -1065,8 +1065,8 @@ <h3 id="igv">IGV<a class="anchor" aria-label="anchor" href="#igv"></a></h3>
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/index.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/index.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 1ab94f1a..aca38597 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -294,8 +294,8 @@ <h4 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/instructor-notes.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index ec5144d4..73c0d71b 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -254,8 +254,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/profiles.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/profiles.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index b0b64915..2bd60781 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -289,7 +289,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/reference.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/teaching_demos.html b/instructor/teaching_demos.html
index 9c5d1a21..79e27c3b 100644
--- a/instructor/teaching_demos.html
+++ b/instructor/teaching_demos.html
@@ -344,7 +344,7 @@ <h4 id="data-analysis-and-visualization-in-r"><a href="https://datacarpentry.org
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/teaching_demos.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-10-02",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 7ca3bec0..193c01a7 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-07-08T22:35Z
+last_built: 2024-07-09T00:03Z
diff --git a/profiles.html b/profiles.html
index d0ae9a9f..17f6a169 100644
--- a/profiles.html
+++ b/profiles.html
@@ -260,8 +260,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/profiles.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/profiles.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-07-08",
-  "datePublished": "2024-07-08"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index ac5b20ae..9718f053 100644
--- a/reference.html
+++ b/reference.html
@@ -293,7 +293,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/reference.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/teaching_demos.html b/teaching_demos.html
index c08e2dda..f3b604ab 100644
--- a/teaching_demos.html
+++ b/teaching_demos.html
@@ -348,7 +348,7 @@ <h4 id="data-analysis-and-visualization-in-r"><a href="https://datacarpentry.org
   "identifier": "https://datacarpentry.github.io/genomics-workshop/teaching_demos.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-10-02",
-  "datePublished": "2024-07-08"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>