Merge pull request #342 from nih-cfde/dev

Feb 2021 Release!!
nih-cfde · Feb 25, 2021 · 5f1556b · 5f1556b
2 parents 6d3089c + 6fc26b9
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diff --git a/.github/action-release-drafter.yml b/.github/action-release-drafter.yml
@@ -10,12 +10,7 @@ categories:
 change-template: '- $TITLE (#$NUMBER)'
 change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
 include-labels:
-   - Oct-2020
-   - Dec-2020
-   - Mar-2021
-   - Jun-2021
-   - Sept-2021
-   - Dec-2021
+   - Training-Release
 
 template: |
   ## Updated

diff --git a/TrainingPlanV3.md b/TrainingPlanV3.md
diff --git a/custom/assets/homepg-images/8.png b/custom/assets/homepg-images/8.png
diff --git a/custom/assets/homepg-images/9.png b/custom/assets/homepg-images/9.png
diff --git a/custom/assets/stylesheets/overrides.min.css b/custom/assets/stylesheets/overrides.min.css
@@ -65,8 +65,13 @@
     break-inside:avoid
 }
 
+.md-announce {
+  background-color: #204060
+}
+
 .md-announce a, .md-announce a:focus, .md-announce a:hover {
-    color:currentColor;
+    color: currentColor;
+
 }
 
 .md-announce strong {
@@ -75,7 +80,7 @@
 
 .md-announce .email {
     margin-left: .6em;
-    color:#C3E1E6
+    color:#ffffff
 }
 .md-announce .twitter {
     margin-left: .6em;
@@ -94,8 +99,10 @@
 
     [data-md-color-scheme=slate] .tx-container {
     background: url("data:image/svg+xml;utf8,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 1123 0'><path d='M1124,2c0,0 0,256 0,256l-1125,0l0,-48c0,0 16,5 55,5c116,0 197,-92 325,-92c121,0 114,46 254,46c140,0 214,-167 572,-166Z' style='fill: hsla(232, 15%, 21%, 1)' /></svg>") repeat bottom, linear-gradient(to bottom, #336699, #33cccc 99%)
+
   }
 
+
 }
 
 .content {
@@ -121,7 +128,7 @@
   }
 
 .content__bottom {
-    align-items: flex-start;
+    align-items: stretch;
     display: flex;
     display: -webkit-flex;
     flex-direction: row;
@@ -137,6 +144,16 @@
     width: 100%;
   }
 
+.data_content_left {
+    flex: 1 1 auto;
+    overflow-y: auto;
+    height: 400px;
+    padding-top: 10px;
+    padding-left: 15px;
+    padding-right: 15px;
+    padding-bottom: 5px;
+    float: center
+  }
 
 @media (min-width:768px) {
     .content__bottom {
@@ -199,8 +216,8 @@
     .tx-hero__image {
         margin-top: 1rem;
         order: 1;
-        max-width: 32rem;
-        transform:translateX(6rem)
+        max-width: 25rem;
+        /*transform:translateX(1rem)*/
 
     }
 
@@ -223,13 +240,14 @@
 
 @media screen and (min-width: 76.25em) {
     .tx-hero__image {
-        transform:translateX(6rem)
+        transform:translateX(1rem)
     }
 }
 
 html {
   box-sizing: inherit;
 
+
 }
 
 *,
@@ -264,8 +282,8 @@ body {
 
 .slider {
   position: relative;
-  width: 700px;
-  height: 350px;
+  width: 50vw;
+  height: 80%;
   max-width: 100vw;
   margin: auto;
   box-shadow: 0 2px 2px 0 rgba(0, 0, 0, 0.14), 0 1px 5px 0 rgba(0, 0, 0, 0.12),
@@ -288,7 +306,7 @@ body {
 }
 
 .slider input[type="radio"] {
-  position: absolute;
+  position:absolute;
   top: 0;
   left: 0;
   opacity: 0;
@@ -351,7 +369,7 @@ body {
 
   display: flex;
   justify-content: space-between;
-  padding: 20px;
+  padding: 10px;
   width: 100%;
   height: 100%;
 
@@ -363,7 +381,10 @@ body {
 
 
 .slide-content {
-  width: 350px;
+  width: 30vw;
+  padding-left: 20px;
+  padding-right: 15px;
+
 }
 
 .slide-title {
@@ -396,9 +417,9 @@ body {
 }
 
 .slide-image img {
+  max-height: 80%;
   max-width: 100%;
-  max-height: 100%;
-  padding-right:10%;
+
 }
 
 /* Slide animations */
@@ -437,6 +458,11 @@ body {
   opacity: 1;
 }
 
+#btn-8:checked ~ .slides .slide:nth-child(8) {
+  transform: translatex(0);
+  opacity: 1;
+}
+
 #btn-1:not(:checked) ~ .slides .slide:nth-child(1) {
   animation-name: swap-out;
   animation-duration: 300ms;
@@ -483,6 +509,14 @@ body {
 
 }
 
+#btn-8:not(:checked) ~ .slides .slide:nth-child(8) {
+  animation-name: swap-out;
+  animation-duration: 300ms;
+  animation-timing-function: linear;
+
+}
+
+
 
 @keyframes swap-out {
   0% {

diff --git a/custom/overrides/home.html b/custom/overrides/home.html
@@ -1,4 +1,5 @@
 {% extends "overrides/main.html" %}
+
 {% block tabs %}
   {{ super() }}
   <link rel="stylesheet" href="{{ 'assets/stylesheets/overrides.min.css' | url }}">
@@ -26,74 +27,84 @@
             </div>
             <ul class="slides">
               <li class="slide">
+                <p class="slide-image">
+                  <img src="{{ 'assets/homepg-images/1.png' | url }}" alt="stuff" width="320" height="240">
+                </p>
                 <div class="slide-content">
                   <h2 class="slide-title">New at CFDE Training</h2>
-                  <p class="slide-text">Explore our latest tutorial additions and </br>discover lessons across a broad spectrum </br>of technical topics.</p>
+                  <p class="slide-text">Explore our latest tutorial additions and discover lessons across a broad spectrum of technical topics.</p>
                   <a href="./Release-Notes/" class="slide-link">Learn More</a>
                 </div>
-                <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/1.png' | url }}" alt="stuff" width="320" height="240">
-                </p>
               </li>
               <li class="slide">
+                <p class="slide-image">
+                  <img src="{{ 'assets/homepg-images/2.png' | url }}" alt="stuff" width="320" height="240">
+                </p>
                 <div class="slide-content">
                   <h2 class="slide-title">GWAS in the Cloud</h2>
-                  <p class="slide-text">Analyse genetic variants to obtain </br>correlations to phenotypes and visualize </br>using a Manhattan plot.</p>
+                  <p class="slide-text">Analyse genetic variants to obtain correlations to phenotypes and visualize using a Manhattan plot.</p>
                   <a href="./Bioinformatics-Skills/GWAS-in-the-cloud/" class="slide-link">Get Started</a>
                 </div>
+              </li>
+              <li class="slide">
                 <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/2.png' | url }}" alt="stuff" width="320" height="240">
+                  <img src="{{ 'assets/homepg-images/8.png' | url }}" alt="stuff" width="320" height="240">
                 </p>
+                <div class="slide-content">
+                  <h2 class="slide-title">RNAseq on Cavatica</h2>
+                  <p class="slide-text">Learn to perform differential gene expression analysis using Kids First cancer cohorts on Cavatica.</p>
+                  <a href="./Bioinformatics-Skills/RNAseq-on-Cavatica/rna_seq_1/" class="slide-link">Get Started</a>
+                </div>
               </li>
               <li class="slide">
+                <p class="slide-image">
+                  <img src="{{ 'assets/homepg-images/3.png' | url }}" alt="stuff" width="320" height="240">
+                </p>
                 <div class="slide-content">
                   <h2 class="slide-title">Amazon Web Services</h2>
-                  <p class="slide-text">Learn to connect, setup and conduct </br>analysis using Amazon's cloud </br>computing services.</p>
+                  <p class="slide-text">Learn to connect, setup and conduct analysis using Amazon's cloud computing services.</p>
                   <a href="./Bioinformatics-Skills/Introduction_to_Amazon_Web_Services/introtoaws1" class="slide-link">Get Started</a>
                 </div>
+              </li>
+              <li class="slide">
                 <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/3.png' | url }}" alt="stuff" width="320" height="240">
+                  <img src="{{ 'assets/homepg-images/9.png' | url }}" alt="stuff" width="320" height="240">
                 </p>
+                <div class="slide-content">
+                  <h2 class="slide-title">Google Cloud Platform</h2>
+                  <p class="slide-text">Learn to setup, download NCBI's SRA datasets and conduct analysis using Google's cloud computing services.</p>
+                  <a href="./Bioinformatics-Skills/Introduction-to-GCP/" class="slide-link">Get Started</a>
+                </div>
               </li>
               <li class="slide">
+                <p class="slide-image">
+                  <img src="{{ 'assets/homepg-images/4.png' | url }}" alt="stuff" width="320" height="240">
+                </p>
                 <div class="slide-content">
                   <h2 class="slide-title">Snakemake Workflows</h2>
-                  <p class="slide-text">Learn to create reproducible and </br>scalable data analyses using the </br>snakemake workflow management </br>system.</p>
+                  <p class="slide-text">Learn to create reproducible and scalable data analyses using the snakemake workflow management system.</p>
                   <a href="./Bioinformatics-Skills/Snakemake/" class="slide-link">Get started</a>
                 </div>
-                <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/4.png' | url }}" alt="stuff" width="320" height="240">
-                </p>
               </li>
               <li class="slide">
+                <p class="slide-image">
+                  <img src="{{ 'assets/homepg-images/5.png' | url }}" alt="stuff" width="320" height="240">
+                </p>
                 <div class="slide-content">
                   <h2 class="slide-title">CFDE Data Portal</h2>
-                  <p class="slide-text">Discover multiple datasets across all </br>Common Fund programs and generate </br>data manifests all in one single search.</p>
+                  <p class="slide-text">Discover multiple datasets across all Common Fund programs and generate data manifests all in one single search.</p>
                   <a href="./Bioinformatics-Skills/CFDE-Portal/" class="slide-link">Get started</a>
                 </div>
-                <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/5.png' | url }}" alt="stuff" width="320" height="240">
-                </p>
               </li>
               <li class="slide">
-                <div class="slide-content">
-                  <h2 class="slide-title">Analysis with Cavatica</h2>
-                  <p class="slide-text">Learn to transfer data subsets </br>between the Kids First portal and </br>Cavatica.</p>
-                  <a href="./Bioinformatics-Skills/Kids-First/KF_7_PushToCavatica/" class="slide-link">Get Started</a>
-                </div>
                 <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/6.png' | url }}" alt="stuff" width="320" height="240">
+                  <img src="{{ 'assets/homepg-images/7.png' | url }}" alt="stuff" width="320" height="240">
                 </p>
-              </li>
-              <li class="slide">
                 <div class="slide-content">
                   <h2 class="slide-title">CFDE Internal Resources</h2>
-                  <p class="slide-text">Find lessons on navigating GitHub, </br>contributing to our websites and </br>identifying MIME type.</p>
+                  <p class="slide-text">Find lessons on navigating GitHub, contributing to our websites and identifying MIME type.</p>
                   <a href="./CFDE-Internal-Training/" class="slide-link">Get Started</a>
                 </div>
-                <p class="slide-image">
-                  <img src="{{ 'assets/homepg-images/7.png' | url }}" alt="stuff" width="320" height="240">
-                </p>
               </li>
             </ul>
           </div>
@@ -106,16 +117,25 @@ <h1>Welcome to CFDE Training Resources!</h1>
       <div class="content__bottom">
         <div class="content__col left">
           <div class="data_header">
-            <p>Past Workshops</p>
-          </div>
-          <div class="data_content">
-            <div style="padding-top: 5px; padding-left: 15px; padding-right: 10px; float: center ">
-              <p><div style="font-size:20px">Introduction to the Kids First Data Resource Portal</div><i>Dec 17,&nbsp;2020 &nbsp;&bull;&nbsp; Virtual Workshop</i><br/><br/>Walk-through of the Kids First Portal to search, filter and visualize data followed by discussion session for next steps to use Kids First data in one's own research.<br/> Workshop Resources:&nbsp; <a href="./Bioinformatics-Skills/Kids-First/Portal-Setup-And-Permissions/KF_3_KF_Registration/" target="_blank" rel="noopener" style="color:#336699;">Setup</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Kids-First/Exploring-Data-in-the-KF-Portal/KF_5_Explore/" target="_blank" rel="noopener" style="color:#336699;">Explore</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Kids-First/Advanced-KF-Portal-Queries/KF_9_AdvancedQuery/" target="_blank" rel="noopener" style="color:#336699;">Queries</a></p>
-            </div>
-            <div style="padding-left: 15px; padding-right: 10px; padding-bottom: 5px; float: center ">
-              <p><div style="font-size:20px">Introduction to Amazon Web Services / Elastic Cloud Computing</div><i>Dec 1,&nbsp;2020 &nbsp;&bull;&nbsp; Virtual Workshop</i><br/><br/>A hands on workshop to introduce cloud computing concepts, create a virtual machine, and run a small job via Amazon Web Services (AWS).<br/> Workshop Resources:&nbsp; <a href="./Bioinformatics-Skills/Introduction_to_Amazon_Web_Services/introtoaws1" target="_blank" rel="noopener" style="color:#336699;">AWS</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Command-Line-BLAST/BLAST1" target="_blank" rel="noopener" style="color:#336699;">BLAST</a></p>
-            </div>
+            <p>Workshops</p>
           </div>
+           <div class="data_content_left">
+             <div>
+              <p><div style="font-size:22px; font-style: italic">Check out our events calendar for <a href="https://www.nih-cfde.org/events/" target="_blank" rel="noopener" style="color:#336699;">upcoming workshops !</a></div></p>
+             </div>
+             <div>
+              <p><div style="font-size:19px">Introduction to Amazon Web Services / Elastic Cloud Computing</div><i>Feb 25,&nbsp;2021 &nbsp;&bull;&nbsp; Virtual Workshop</i><br/><br/>A hands-on workshop to introduce cloud computing concepts, create a virtual machine, and run a small job via Amazon Web Services (AWS).<br/> Workshop Resources:&nbsp; <a href="./Bioinformatics-Skills/Introduction_to_Amazon_Web_Services/introtoaws1" target="_blank" rel="noopener" style="color:#336699;">AWS</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Command-Line-BLAST/BLAST1" target="_blank" rel="noopener" style="color:#336699;">BLAST</a></p>
+             </div>
+             <div>
+              <p><div style="font-size:19px">Introduction to Amazon Web Services / Elastic Cloud Computing</div><i>Jan 29,&nbsp;2021 &nbsp;&bull;&nbsp; Virtual Workshop</i><br/><br/>A hands-on workshop to introduce cloud computing concepts, create a virtual machine, and run a small job via Amazon Web Services (AWS).<br/> Workshop Resources:&nbsp; <a href="./Bioinformatics-Skills/Introduction_to_Amazon_Web_Services/introtoaws1" target="_blank" rel="noopener" style="color:#336699;">AWS</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Command-Line-BLAST/BLAST1" target="_blank" rel="noopener" style="color:#336699;">BLAST</a></p>
+             </div>
+             <div>
+              <p><div style="font-size:19px">Introduction to the Kids First Data Resource Portal</div><i>Dec 17,&nbsp;2020 &nbsp;&bull;&nbsp; Virtual Workshop</i><br/><br/>Walk-through of the Kids First Portal to search, filter and visualize data followed by discussion session for next steps to use Kids First data in one's own research.<br/> Workshop Resources:&nbsp; <a href="./Bioinformatics-Skills/Kids-First/Portal-Setup-And-Permissions/KF_3_KF_Registration/" target="_blank" rel="noopener" style="color:#336699;">Setup</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Kids-First/Exploring-Data-in-the-KF-Portal/KF_5_Explore/" target="_blank" rel="noopener" style="color:#336699;">Explore</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Kids-First/Advanced-KF-Portal-Queries/KF_9_AdvancedQuery/" target="_blank" rel="noopener" style="color:#336699;">Queries</a></p>
+             </div>
+             <div>
+              <p><div style="font-size:19px">Introduction to Amazon Web Services / Elastic Cloud Computing</div><i>Dec 1,&nbsp;2020 &nbsp;&bull;&nbsp; Virtual Workshop</i><br/><br/>A hands-on workshop to introduce cloud computing concepts, create a virtual machine, and run a small job via Amazon Web Services (AWS).<br/> Workshop Resources:&nbsp; <a href="./Bioinformatics-Skills/Introduction_to_Amazon_Web_Services/introtoaws1" target="_blank" rel="noopener" style="color:#336699;">AWS</a> &nbsp;&bull;&nbsp; <a href="./Bioinformatics-Skills/Command-Line-BLAST/BLAST1" target="_blank" rel="noopener" style="color:#336699;">BLAST</a></p>
+             </div>
+           </div>
         </div>
         <div class="content__col middle">
           <div class="data_header">

diff --git a/custom/overrides/main.html b/custom/overrides/main.html
@@ -1,5 +1,4 @@
 {% extends "base.html" %}
-
 {% block announce %}
   <a href="mailto:CFDE-HelpDesk%20<[email protected]">
     <strong>For suggestions and questions, contact us! </strong>
@@ -18,7 +17,6 @@
     </span>
   </a>
 {% endblock %}
-
 {% block footer %}
 {% import "partials/language.html" as lang with context %}
  <footer class="md-footer">
@@ -33,3 +31,21 @@
   </div>
  </footer>
 {% endblock %}
+{% block analytics %}
+  {{ super() }}
+  <!-- Matomo -->
+  <script type="text/javascript">
+    var _paq = window._paq = window._paq || [];
+    /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+    _paq.push(['trackPageView']);
+    _paq.push(['enableLinkTracking']);
+    (function() {
+      var u="https://nihcfde.matomo.cloud/";
+      _paq.push(['setTrackerUrl', u+'matomo.php']);
+      _paq.push(['setSiteId', '3']);
+      var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0];
+      g.type='text/javascript'; g.async=true; g.src='//cdn.matomo.cloud/nihcfde.matomo.cloud/matomo.js'; s.parentNode.insertBefore(g,s);
+    })();
+  </script>
+  <!-- End Matomo Code -->
+{% endblock %}
diff --git a/custom/partials/nav.html b/custom/partials/nav.html