Merge branch 'galaxyproject:main' into Filter,-Plot,-and-Explore_WIP

_includes/pathway-card.html

@@ -0,0 +1,32 @@
+{% assign path = include.path %}
+
+{% assign coverimage = path.coverimage | default: "/assets/images/GTNLogo1000.png" %}
+{% assign coverimagealt = path.coverimagealt | default: "GTN logo with a multi-coloured star and the words Galaxy Training Network"%}
+
+
+  <div class="pathwayitem col-md-4">
+    <a href="{{site.baseurl}}{{path.url}}">
+    <div class="card d-flex">
+      <div class="d-flex align-items-center" style="height:200px;">
+      {% if path.cover-image %}
+      <img class="pathwaycover card-img-top" src="{{site.baseurl}}/{{path.cover-image}}" alt="{{ path.cover-image-alt }}" loading="lazy">
+      {% else %}
+      <img class="pathwaycover card-img-top" src="{{site.baseurl}}{{coverimage}}" alt="{{ coverimagealt }}" loading="lazy">
+      {% endif %}
+      </div>
+      <div class="card-body d-flex flex-column">
+        <h5 class="card-title">{{path.title}}</h5>
+        <p class="card-text">
+          {{path.description}}
+        </p>
+      </div>
+      <div class="card-footer">
+        {% for tag in path.tags %}
+        <span class="label label-default tutorial_tag" style="{{ tag | colour_tag }}">{{ tag }}</span>
+        {% endfor %}
+      </div>
+    </div>
+    </a>
+  </div>
+
+

assets/css/main.scss

@@ -572,27 +572,40 @@ blockquote {
 	}
 }
 
-.pathway{
+.pathwaylist{
     display: flex;
     flex-wrap: wrap;
     flex-direction: row;
     justify-content: space-around;
     margin-bottom: 2rem;
 
     .pathwayitem {
-      width: 100%;
       background: transparent;
-      border: 1px solid var(--border-light);
+
+      .card{
+        margin-bottom: 1em;
+      }
+      .card-body{
+        height: 17rem;
+        overflow: hidden;
+      }
+      .card-text{
+        margin: 1rem;
+        vertical-align: center;
+      }
+      .card-title{
+        height: 5rem;
+      }
       .card-header {
-	background: var(--brand-color);
-	border-bottom: 1px solid var(--border-light);
+	    background: var(--brand-color);
+	    border-bottom: 1px solid var(--border-light);
       }
     }
     .pathwaycover {
         width: 100%;
-        object-fit: cover;
-        margin-top: auto;
-        margin-bottom: auto;
+        max-height: 100%;
+        object-fit: contain;
+        margin-top: 1em;
         background-color: white;
         border-radius: 2rem;;
         padding: 1rem;

learning-pathways/admin-training.md

@@ -1,6 +1,7 @@
 ---
 layout: learning-pathway
 title: Admin Training Course
+type: admin-dev
 description: |
   Learn how to setup, configure, and maintain your own Galaxy server. This learning pathway
   will guide you through all the steps required to setup your own Galaxy server with Ansible,

learning-pathways/climate-learning.md

@@ -0,0 +1,26 @@
+---
+layout: learning-pathway
+
+title: Discovering galaxy through climate analysis
+description: |
+  How to have a complete overview of how Galaxy works going from the user welcome page to use batch tools and finishing by conducting interactive analysis. These set of 3 Climate tutorials allow you to understand and see plenty of the multiple features of Galaxy and learning about the cool subject of climate analysis. 
+tags: [Climate, Overview]
+
+
+pathway:
+  - section: "Following 3 climate tutorials"
+    description: |
+      During this session you will first learn about the galaxy interface and how to use batch tools. Then, you'll be able to run through a jupyter notebook launch from Galaxy. Finally, you will conduct a climate analysis on a desktop application with Panoply.
+    tutorials:
+      - name: pangeo
+        topic: climate
+      - name: pangeo-notebook
+        topic: climate
+      - name: panoply
+        topic: climate
+
+---
+
+This can be done in less than 3h. To be really complete you can then create a workflow from the history of your 1st tutorial and show how workflows work.
+
+

learning-pathways/genome-annotation-eukaryote.md

@@ -3,6 +3,7 @@ layout: learning-pathway
 title: Genome annotation for eukaryotes
 description: |
   Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo.
+type: use
 tags: [genome annotation, eukaryote]
 
 cover-image: assets/images/gga.png
@@ -12,6 +13,8 @@ maintainers:
 funding:
 - erasmusplus
 
+
+
 pathway:
   - section: "Module 1: Introduction"
     description: |

learning-pathways/genome-annotation-prokaryote.md

@@ -3,6 +3,7 @@ layout: learning-pathway
 title: Genome annotation for prokaryotes
 description: |
   Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo.
+type: use
 tags: [genome annotation, prokaryote]
 
 cover-image: assets/images/gga.png

learning-pathways/index.md

@@ -2,46 +2,40 @@
 layout: page
 ---
 
-{% assign pathways = site.pages | where: "layout", "learning-pathway" | sort: "priority", "last" %}
+{% assign pathways_science = site.pages | where: "layout", "learning-pathway" | where: "type", "use" | sort: "priority", "last" %}
+
+{% assign pathways_other = site.pages | where: "layout", "learning-pathway" | where_exp: "item", "item.type != 'use'" | sort: "priority", "last" %}
 
 
 # Learning Pathways
 
 Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway.
 
+## For Scientists
+
+
 <!-- list all available pathways as cards  -->
-<div class="pathway">
-{% for path in pathways %}
-
-{% assign coverimage = path.coverimage | default: "/assets/images/GTNLogo1000.png" %}
-{% assign coverimagealt = path.coverimagealt | default: "GTN logo with a multi-coloured star and the words Galaxy Training Network"%}
-<div class="card pathwayitem">
- <div class="card-header">
-   <a href="{{site.baseurl}}{{path.url}}"><h3 class="card-title">{{path.title}}</h3></a>
- </div>
- <div class="row no-gutters">
-  <div class="col-sm-5">
-   {% if path.cover-image %}
-   <img class="card-img pathwaycover" src="{{site.baseurl}}/{{path.cover-image}}" alt="{{ path.cover-image-alt }}" loading="lazy">
-   {% else %}
-   <img class="card-img pathwaycover" src="{{site.baseurl}}{{coverimage}}" alt="{{ coverimagealt }}" loading="lazy">
-   {% endif %}
-  </div>
-  <div class="col-sm-7">
-   <div class="card-body">
-   <p></p>
-   {% for tag in path.tags %}
-   <span class="label label-default tutorial_tag" style="{{ tag | colour_tag }}">{{ tag  }}</span>
-    {% endfor %}
-   <hr/>
-   <p class="card-text">
-     {{ path.description }}
-   </p>
-   <a href="{{site.baseurl}}{{path.url}}" class="btn btn-primary">View Learning Pathway</a>
-   </div>
-  </div>
- </div>
+<div class="pathwaylist row">
+
+
+{% for path in pathways_science %}
+
+{% include _includes/pathway-card.html path=path %}
+
+{% endfor %}
+
 </div>
 
+
+## For Teachers, Developers and System Administrators
+
+<!-- list all available pathways as cards  -->
+<div class="pathwaylist row">
+
+{% for path in pathways_other %}
+
+{% include _includes/pathway-card.html path=path %}
+
 {% endfor %}
+
 </div>

learning-pathways/intro-to-galaxy-and-ecology.md

@@ -1,17 +1,23 @@
 ---
 layout: learning-pathway
+type: use
+
+title: Introduction to Galaxy and Ecological data analysis
+description: |
+  This learning path aims to teach you the basics of Galaxy and analysis of ecological data.
+  You will learn how to use Galaxy for analysis, and will be guided through the common
+  steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling.
+
+
 tags: [beginner]
+cover-image: assets/images/galaxy-e-logo.png
+cover-image-alt: "Drawing of an Ecological System"
 
 maintainers:
 - yvanlebras
 funding:
 - erasmusplus
 
-title: Introduction to Galaxy and Ecological data analysis
-description: |
-  This learning path aims to teach you the basics of Galaxy and analysis of ecological data.
-  You will learn how to use Galaxy for analysis, and will be guided through the common
-  steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling.
 
 pathway:
   - section: "Module 1: Introduction to Galaxy"

learning-pathways/intro-to-galaxy-and-genomics.md

@@ -1,6 +1,7 @@
 ---
 layout: learning-pathway
 tags: [beginner]
+type: use
 
 maintainers:
 - shiltemann

learning-pathways/intro-to-r-and-ml.md

@@ -1,6 +1,7 @@
 ---
 layout: learning-pathway
 tags: [beginner]
+type: use
 
 maintainers:
 - fpsom

learning-pathways/metagenomics.md

@@ -1,5 +1,8 @@
 ---
 layout: learning-pathway  # (uncomment this line to activate it)
+type: use
+cover-image: assets/images/microgalaxy-logo.png
+cover-image-alt: "microgalaxy logo"
 
 maintainers:
 - bebatut
@@ -54,7 +57,7 @@ pathway:
     description: |
         This module covers the following questions:
         - Which species (or genera, families, ...) are present in my sample?
-        - What are the different approaches and tools to get the community profile of my sample? 
+        - What are the different approaches and tools to get the community profile of my sample?
         - How can we visualize and compare community profiles?
 
         This module will cover taxonomic profiling in theory and also with an example tutorial.
@@ -67,15 +70,15 @@ pathway:
         #description: Application tutorial
 
   #- section: "Module 6: Taxonomic binning"
-  #  description: 
+  #  description:
   #
   #  tutorials:
   #    - name: learner_participation_engagement
   #      topic: metagenomics
 
-  
+
   #- section: "Module 7: Community Biodiversity"
-  #  description: 
+  #  description:
   #
   #  tutorials:
   #    - name: learner_participation_engagement

learning-pathways/pathway-example.md

@@ -6,6 +6,8 @@ description: |
   Description of the pathway. What will be covered, what are the learning objectives, etc?
   Make this as thorough as possible, 1-2 paragraphs. This appears on the index page that
   lists all the learning paths, and at the top of the pathway page
+
+type: use  # 'use' for science topics, or admin-dev or instructors
 tags: [some, keywords, here ]
 
 cover-image: assets/images/gat.png # optional, define your own cover image for the pathway index page, default is the GTN logo

learning-pathways/train-the-trainers.md

@@ -1,5 +1,6 @@
 ---
 layout: learning-pathway  # (uncomment this line to activate it)
+type: instructors
 
 title: Train the Trainers
 description: |

topics/admin/tutorials/backup-cleanup/tutorial.md

@@ -129,7 +129,7 @@ tutorial]({% link topics/admin/tutorials/gxadmin/tutorial.md %}).
 >    +        user: galaxy # Run as the Galaxy user
 >    +        minute: "0"
 >    +        hour: "0"
->    +        job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60"
+>    +        job: "SHELL=/bin/bash source {{ galaxy_venv_dir }}/bin/activate &&  GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server GALAXY_CONFIG_FILE={{ galaxy_config_file }} /usr/local/bin/gxadmin galaxy cleanup 60"
 >    {% endraw %}
 >    ```
 >    {: data-commit="Configure gxadmin to cleanup data"}