diff --git a/404.html b/404.html
index 8999bc3d..2a755bc8 100644
--- a/404.html
+++ b/404.html
@@ -222,8 +222,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/AMI-setup.html b/AMI-setup.html
index 99d698fa..cab009e0 100644
--- a/AMI-setup.html
+++ b/AMI-setup.html
@@ -280,7 +280,7 @@ <h4 id="sign-into-aws-and-launch-an-instance">Sign into AWS and Launch an Instan
<h3 class="accordion-header" id="headingSpoiler1">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>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
@@ -335,7 +335,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler2">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>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>
@@ -476,7 +476,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index cd115efa..7234aeb0 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -249,7 +249,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 7ad681b2..59eb1ef0 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -301,7 +301,7 @@ <h1>Licenses</h1>
"identifier": "https://datacarpentry.github.io/genomics-workshop/LICENSE.html",
"dateCreated": "2015-06-03",
"dateModified": "2023-09-19",
- "datePublished": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/faq.html b/faq.html
index dad88c28..29ff6dd3 100644
--- a/faq.html
+++ b/faq.html
@@ -423,7 +423,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/index.html b/index.html
index 75cb82fd..5eafc5ac 100644
--- a/index.html
+++ b/index.html
@@ -346,7 +346,7 @@ <h2 id="required-additional-software">Required additional software<a class="anch
<h3 class="accordion-header" id="headingSpoiler1">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Windows</h3>
</button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
<div class="accordion-body">
<ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
LibreOffice installation page</a>. The version for Windows should
@@ -424,7 +424,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
<h3 class="accordion-header" id="headingSpoiler2">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Mac OS X</h3>
</button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
<div class="accordion-body">
<ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
LibreOffice installation page</a>. The version for Mac should
@@ -444,7 +444,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
<h3 class="accordion-header" id="headingSpoiler3">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Linux</h3>
</button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
<div class="accordion-body">
<ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
LibreOffice installation page</a>. The version for Linux should
@@ -562,7 +562,7 @@ <h3 id="conda">Conda<a class="anchor" aria-label="anchor" href="#conda"></a></h3
<h3 class="accordion-header" id="headingSpoiler4">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Linux</h3>
</button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
<div class="accordion-body">
<p>To install Conda, type:</p>
<div class="codewrapper sourceCode" id="cb1">
@@ -583,7 +583,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler5">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
<div class="accordion-body">
<p>To install Conda, type:</p>
<div class="codewrapper sourceCode" id="cb2">
@@ -607,7 +607,7 @@ <h3 id="fastqc">FastQC<a class="anchor" aria-label="anchor" href="#fastqc"></a><
<h3 class="accordion-header" id="headingSpoiler6">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
<div class="accordion-body">
<p>To install FastQC, type:</p>
<div class="codewrapper sourceCode" id="cb3">
@@ -625,7 +625,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler7">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>FastQC Source Code Installation</h3>
</button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
<div class="accordion-body">
<p>If you prefer to install from source, follow the directions
below:</p>
@@ -669,7 +669,7 @@ <h3 id="trimmomatic">Trimmomatic<a class="anchor" aria-label="anchor" href="#tri
<h3 class="accordion-header" id="headingSpoiler8">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
<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>
@@ -686,7 +686,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler9">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Trimmomatic Source Code Installation</h3>
</button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
<div class="accordion-body">
<p>If you prefer to install from source, follow the directions
below:</p>
@@ -723,7 +723,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler10">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Simplify the Invocation, or to Test your installation if you installed with miniconda3:</h3>
</button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
<div class="accordion-body">
<p>To simplify the invocation you could also create a script in the
~/bin folder:</p>
@@ -753,7 +753,7 @@ <h3 id="bwa">BWA<a class="anchor" aria-label="anchor" href="#bwa"></a></h3>
<h3 class="accordion-header" id="headingSpoiler11">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
<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>
@@ -770,7 +770,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler12">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>BWA Source Code Installation</h3>
</button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
<div class="accordion-body">
<p>If you prefer to install from source, follow the instructions
below:</p>
@@ -803,7 +803,7 @@ <h3 id="samtools">SAMtools<a class="anchor" aria-label="anchor" href="#samtools"
<h3 class="accordion-header" id="headingSpoiler13">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
<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>
@@ -836,7 +836,7 @@ <h3 class="callout-title">SAMtools Versions<a class="anchor" aria-label="anchor"
<h3 class="accordion-header" id="headingSpoiler14">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>SAMtools Source Code Installation</h3>
</button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
<div class="accordion-body">
<p>If you prefer to install from source, follow the instructions
below:</p>
@@ -875,7 +875,7 @@ <h3 id="bcftools">BCFtools<a class="anchor" aria-label="anchor" href="#bcftools"
<h3 class="accordion-header" id="headingSpoiler15">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
<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>
@@ -892,7 +892,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler16">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>BCF tools Source Code Installation</h3>
</button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
<div class="accordion-body">
<p>If you prefer to install from source, follow the instructions
below:</p>
@@ -976,8 +976,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 1e3d22c0..22d9db43 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -249,8 +249,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 0c360a9f..9f5528c0 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -216,8 +216,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/AMI-setup.html b/instructor/AMI-setup.html
index f8cffa0d..338e741f 100644
--- a/instructor/AMI-setup.html
+++ b/instructor/AMI-setup.html
@@ -276,7 +276,7 @@ <h4 id="sign-into-aws-and-launch-an-instance">Sign into AWS and Launch an Instan
<h3 class="accordion-header" id="headingSpoiler1">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>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
@@ -331,7 +331,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler2">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>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>
@@ -472,7 +472,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 1ae8964e..490f0498 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -245,7 +245,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index f35acea4..c1163f83 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -297,7 +297,7 @@ <h1>Licenses</h1>
"identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/LICENSE.html",
"dateCreated": "2015-06-03",
"dateModified": "2023-09-19",
- "datePublished": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/faq.html b/instructor/faq.html
index c1700d5b..25aba096 100644
--- a/instructor/faq.html
+++ b/instructor/faq.html
@@ -419,7 +419,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/index.html b/instructor/index.html
index b155355a..9185733e 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -345,7 +345,7 @@ <h2 id="required-additional-software">Required additional software<a class="anch
<h3 class="accordion-header" id="headingSpoiler1">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Windows</h3>
</button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
<div class="accordion-body">
<ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
LibreOffice installation page</a>. The version for Windows should
@@ -423,7 +423,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
<h3 class="accordion-header" id="headingSpoiler2">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Mac OS X</h3>
</button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
<div class="accordion-body">
<ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
LibreOffice installation page</a>. The version for Mac should
@@ -443,7 +443,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
<h3 class="accordion-header" id="headingSpoiler3">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Linux</h3>
</button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
<div class="accordion-body">
<ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
LibreOffice installation page</a>. The version for Linux should
@@ -561,7 +561,7 @@ <h3 id="conda">Conda<a class="anchor" aria-label="anchor" href="#conda"></a></h3
<h3 class="accordion-header" id="headingSpoiler4">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Linux</h3>
</button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
<div class="accordion-body">
<p>To install Conda, type:</p>
<div class="codewrapper sourceCode" id="cb1">
@@ -582,7 +582,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler5">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
<div class="accordion-body">
<p>To install Conda, type:</p>
<div class="codewrapper sourceCode" id="cb2">
@@ -606,7 +606,7 @@ <h3 id="fastqc">FastQC<a class="anchor" aria-label="anchor" href="#fastqc"></a><
<h3 class="accordion-header" id="headingSpoiler6">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
<div class="accordion-body">
<p>To install FastQC, type:</p>
<div class="codewrapper sourceCode" id="cb3">
@@ -624,7 +624,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler7">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>FastQC Source Code Installation</h3>
</button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
<div class="accordion-body">
<p>If you prefer to install from source, follow the directions
below:</p>
@@ -668,7 +668,7 @@ <h3 id="trimmomatic">Trimmomatic<a class="anchor" aria-label="anchor" href="#tri
<h3 class="accordion-header" id="headingSpoiler8">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
<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>
@@ -685,7 +685,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler9">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Trimmomatic Source Code Installation</h3>
</button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
<div class="accordion-body">
<p>If you prefer to install from source, follow the directions
below:</p>
@@ -722,7 +722,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler10">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Simplify the Invocation, or to Test your installation if you installed with miniconda3:</h3>
</button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
<div class="accordion-body">
<p>To simplify the invocation you could also create a script in the
~/bin folder:</p>
@@ -752,7 +752,7 @@ <h3 id="bwa">BWA<a class="anchor" aria-label="anchor" href="#bwa"></a></h3>
<h3 class="accordion-header" id="headingSpoiler11">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
<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>
@@ -769,7 +769,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler12">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>BWA Source Code Installation</h3>
</button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
<div class="accordion-body">
<p>If you prefer to install from source, follow the instructions
below:</p>
@@ -802,7 +802,7 @@ <h3 id="samtools">SAMtools<a class="anchor" aria-label="anchor" href="#samtools"
<h3 class="accordion-header" id="headingSpoiler13">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
<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>
@@ -835,7 +835,7 @@ <h3 class="callout-title">SAMtools Versions<a class="anchor" aria-label="anchor"
<h3 class="accordion-header" id="headingSpoiler14">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>SAMtools Source Code Installation</h3>
</button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
<div class="accordion-body">
<p>If you prefer to install from source, follow the instructions
below:</p>
@@ -874,7 +874,7 @@ <h3 id="bcftools">BCFtools<a class="anchor" aria-label="anchor" href="#bcftools"
<h3 class="accordion-header" id="headingSpoiler15">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>MacOS</h3>
</button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
<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>
@@ -891,7 +891,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
<h3 class="accordion-header" id="headingSpoiler16">
<div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>BCF tools Source Code Installation</h3>
</button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
<div class="accordion-body">
<p>If you prefer to install from source, follow the instructions
below:</p>
@@ -975,8 +975,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index a2f15f5d..14202990 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -243,8 +243,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 54568ef3..45d19578 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -203,8 +203,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index b1ddd202..c88f7d14 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -238,7 +238,7 @@ <h1>Glossary</h1>
"identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/reference.html",
"dateCreated": "2015-06-03",
"dateModified": "2023-09-19",
- "datePublished": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/instructor/teaching_demos.html b/instructor/teaching_demos.html
index 7ef13af9..7b9dcab5 100644
--- a/instructor/teaching_demos.html
+++ b/instructor/teaching_demos.html
@@ -293,7 +293,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index daf1276e..4e19b424 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-05-07T00:18Z
+last_built: 2024-05-14T00:17Z
diff --git a/profiles.html b/profiles.html
index b67b5dd1..b5ef0788 100644
--- a/profiles.html
+++ b/profiles.html
@@ -209,8 +209,8 @@ <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": "2024-05-07",
- "datePublished": "2024-05-07"
+ "dateModified": "2024-05-14",
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/reference.html b/reference.html
index c0906e61..64d675b8 100644
--- a/reference.html
+++ b/reference.html
@@ -242,7 +242,7 @@ <h1>Glossary</h1>
"identifier": "https://datacarpentry.github.io/genomics-workshop/reference.html",
"dateCreated": "2015-06-03",
"dateModified": "2023-09-19",
- "datePublished": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>
diff --git a/teaching_demos.html b/teaching_demos.html
index cb1563fd..5dfa5675 100644
--- a/teaching_demos.html
+++ b/teaching_demos.html
@@ -297,7 +297,7 @@ <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": "2024-05-07"
+ "datePublished": "2024-05-14"
}
</script><script>