Merge branch 'main' into spoc_2024_end

CONTRIBUTORS.yaml

@@ -707,6 +707,12 @@ dyusuf:
     affiliations:
       - uni-freiburg
 
+dometto:
+    name: Dawa Ometto
+    joined: 2024-12
+    affiliations:
+      - surf
+
 eancelet:
     name: Estelle Ancelet
     email: [email protected]
@@ -1694,6 +1700,12 @@ miRlyKayleigh:
     email: [email protected]
     joined: 2022-12
 
+mirelaminkova:
+    name: Mirela Minkova
+    joined: 2024-12
+    affiliations:
+      - surf
+
 moffmade:
     name: Cory Maughmer
     joined: 2018-06
@@ -2696,6 +2708,10 @@ yvesvdb:
     affiliations:
       - ifb
 
+yuliiaorlova:
+    name: Yuliia Orlova
+    joined: 2024-12
+
 zargham-ahmad:
     name: Zargham Ahmad
     email: [email protected]

ORGANISATIONS.yaml

@@ -318,6 +318,14 @@ swiss-tph:
     github: false
     ror: "03adhka07"
 
+surf:
+    short_name: SURF
+    name: SURF
+    url: https://www.surf.nl/
+    avatar: "/training-material/shared/images/surf.png"
+    github: false
+    ror: "009vhk114"
+
 tb-capt:
     short_name: TB-CAPT
     name: TB-CAPT

_layouts/event.html

@@ -173,13 +173,14 @@ <h3>Get set up for the course!</h3>
     <p>Follow the steps below to get set up with everything you need to participate in the course!</p>
 
     <!-- Galaxy setup -->
-    {% unless event.infrastructure.no_galaxy %}
+    {% if event.infrastructure.servers %}
     <div class="card setup-card">
 	  <div class="row no-gutters">
 		<div class="col-sm-3">
 		  <img src="{% link assets/images/galaxylogo.png %}" class="card-img" alt="Galaxy logo" style="max-height: 10em">
 		</div>
 		<div class="col-sm-9">
+
 		  <div class="card-body">
 			<h5 class="card-title">Create a Galaxy Account</h5>
 			<p class="card-text">
@@ -200,7 +201,7 @@ <h5 class="card-title">Create a Galaxy Account</h5>
 		</div>
 	  </div>
 	</div>
-	{% endunless %}
+	{% endif %}
 
     <!-- TIaaS setup -->
     {% if event.infrastructure.tiaas %}

_plugins/api.rb

@@ -279,7 +279,9 @@ def generate(site)
 
 
 Jekyll::Hooks.register :site, :post_read do |site|
-  Gtn::Hooks.by_tool(site)
+  if Jekyll.env == 'production'
+    Gtn::Hooks.by_tool(site)
+  end
 end
 
 # Basically like `PageWithoutAFile`, we just write out the ones we'd created earlier.

bin/schema-event.yaml

@@ -320,10 +320,6 @@ mapping:
                 type: str
                 description: |
                   Custom markdown formatted text to display. Note that Jekyll things like `{% snippet %}` or `{% include %}` will not work here.
-          no_galaxy:
-            type: bool
-            description: |
-              Set to `true` to disable the automatic "register for a galaxy account" card.
     tags:
         type: seq
         sequence:

events/2025-01-28-src.md

@@ -0,0 +1,105 @@
+---
+layout: event
+
+# Status of this page, remove these lines when ready
+draft: true  
+status: wip  
+
+# Description of your event
+title: Galaxy at SURF Research Cloud workshop
+description: |
+  Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. 
+
+
+
+# Practical Information
+date_start: 2025-01-28
+
+cost: free 
+audience: This event is targeted towards researchers in the Netherlands who already have experience working with Galaxy. 
+contact_email: [email protected]
+async: false 
+mode: onsite
+
+registration:
+  message: Please send an email to [email protected] to register for the workshop!
+  deadline: 2025-01-10
+  open: true 
+
+# Location of the event
+# For online events, just the 'name' is enough
+location:
+  name: SURF Amsterdam  
+  address: Science Park 140
+  city: Amsterdam
+  country: The Netherlands
+  postcode: 1098 XG
+
+
+
+# People involved, organisers, speakers, funders, etc
+# Must be defined in CONTRIBUTORS.yaml file
+contributions:
+  organisers:
+  - mirelaminkova
+  instructors:
+  - mirelaminkova
+  - yuliiaorlova
+  funding:
+  - surf 
+
+
+# Galaxy and other infrastructure that will be used for your event.
+# This will be used to create the setup instructions for participants
+infrastructure:
+  tiaas: false   
+  custom: 
+    description: |
+      Before joining the course, please make sure to:
+        - Bring a laptop with at least 8GB of RAM.
+        - Do the [Intro to Galaxy](http://training.galaxyproject.org/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) tutorial if you are not yet familiar with Galaxy
+        - Up-to-date browser
+        - Experience in using SURF Research Cloud 
+
+# Program of your course
+# Add GTN tutorials by supplying the topic and tutorial name
+# For non-GTN sessions, add a "type:custom" session and description
+program:
+  - section: "Galaxy & Pulsar on SURF"  # section title is optional
+    description: |
+      During the workshop, you will see a short demo and get a chance to test the catalog item yourself.
+    tutorials:
+      - name: SURF SRC introduction
+        type: custom
+        time: "13:00 - 13:40"
+
+      - name: surf-research-cloud-galaxy
+        topic: admin
+        time: "13:40 - 14:10"
+
+      - name: surf-research-cloud-pulsar
+        topic: admin
+        time: "14:10 - 14:40"
+
+      - type: custom
+        name: Coffee Break
+        time: "14:40"
+      - name: mapping
+        topic: sequence-analysis
+        time: "14:40 - 15:40"
+
+      - name: general-introduction
+        topic: assembly
+        time: "15:40 - 16:10"
+
+      - type: custom
+        name: General feedback from participants 
+        time: "16:10"
+
+      - type: custom
+        name: Borreltje
+        time: "16:30 - 17:00"
+
+---
+
+During the workshop, you will see a short demo and get a chance to test the catalog item yourself. This will be followed by a discussion about your needs as Galaxy researchers, helping us work toward a better future for the Dutch research community. We will conclude the day with drinks and networking with fellow Galaxy NL users.

events/2025-02-04-biont-software-best-practice.md

@@ -0,0 +1,18 @@
+---
+layout: event-external
+title: "Code & Collaborate: The FAIRytale of Software Development"
+external: "https://www.cecam.org/workshop-details/code-collaborate-the-fairytale-of-software-development-1447"
+description: | 
+    Calling all learners! Join us for our #BioNT workshop on software best practices. This three-day workshop will 
+    cover collaborative software development, version control, code review, robust software testing, and much more. 
+    Register by January 20th.
+date_start: 2025-02-04
+date_end: 2025-02-06
+contributions:
+  organisers:
+    - teresa-m
+  funding:
+    - biont
+location:
+  name: Online
+---

news/_posts/2024-12-17-gta-feedback.md

@@ -0,0 +1,17 @@
+---
+title: "Organizing GTA2025: Give us feedback and your availability!"
+contributions:
+  authorship: [teresa-m]
+tags: [gtn, event]
+layout: news
+cover: "events/images/galaxy-academy-logo.png"
+coveralt: "A laptop displaying shapes resembling a statistical plot with a program from Galaxy Training Academy. Surrounding the laptop, there are DNA strands as well as a pen displayed."
+---
+
+# Give us feedback and your availability for the GTA 2025
+
+As the end of the year is approaching rapidly, we are excited to announce:
+
+🎉We have decided to host the next Galaxy Training Academy in Spring 2025!🎉
+
+The GTA is only possible through community effort, and we will need all of you again to help make the GTA a success. Therefore, we are asking you to fill out this [Form](https://docs.google.com/forms/d/e/1FAIpQLSf_DVEdf7n9MWJe7XLa3UTPGMNE9y-F8S-EHXRrZ-twNETYrg/viewform) by the 20th of December. Here, you can provide feedback on what to improve, your availability for potential GTA weeks, and how you would like to contribute.

topics/admin/tutorials/beacon/tutorial.md

@@ -330,7 +330,7 @@ Now that our beacon is running, we need to get data from Galaxy to the Beacon
 >    ```diff
 >    --- a/templates/nginx/galaxy.j2
 >    +++ b/templates/nginx/galaxy.j2
->    @@ -115,4 +115,14 @@ server {
+>    @@ -117,4 +117,14 @@ server {
 >     
 >     	{{ tiaas_nginx_routes }}
 >     

topics/admin/tutorials/connect-to-compute-cluster/tutorial.md

@@ -148,7 +148,7 @@ be taken into consideration when choosing where to run jobs and what parameters
 >    @@ -194,6 +194,16 @@ nginx_ssl_role: usegalaxy_eu.certbot
 >     nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem
 >     nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-www-data.pem
->
+>     
 >    +# Slurm
 >    +slurm_roles: ['controller', 'exec'] # Which roles should the machine play? exec are execution hosts.
 >    +slurm_nodes:

topics/admin/tutorials/monitoring/tutorial.md

@@ -535,15 +535,15 @@ There are some nice examples of dashboards available from the public Galaxies, w
 >    ```diff
 >    --- a/templates/nginx/galaxy.j2
 >    +++ b/templates/nginx/galaxy.j2
->    @@ -108,4 +108,9 @@ server {
->     		proxy_pass http://{{ galaxy_config.gravity.reports.bind }}:/;
+>    @@ -109,4 +109,9 @@ server {
+>     		proxy_set_header X-Forwarded-Host $host;
+>     		proxy_set_header X-Forwarded-Proto $scheme;
 >     	}
->     
+>    +
 >    +	location /grafana/ {
 >    +		proxy_pass http://127.0.0.1:3000/;
 >    +		proxy_set_header Host $http_host;
 >    +	}
->    +
 >     }
 >    {% endraw %}
 >    ```

topics/admin/tutorials/reports/tutorial.md

@@ -32,17 +32,6 @@ requirements:
 
 The reports application gives some pre-configured analytics screens. These are very easy to setup and can help with debugging issues in Galaxy.
 
-> <warning-title>Currently Broken, Requires Separate Domain</warning-title>
-> Reports does not work, under a path prefix (the default setup that most
-> people will use.) It is completely broken and the developers have no plans to fix it in the near term.
-> See
-> [galaxyproject/galaxy#15966](https://github.com/galaxyproject/galaxy/issues/15966) for more details.
->
-> However, it should still function with a separate domain, if that is possible
-> for your setup. Otherwise, it **will not work.** If you wish to follow this
-> tutorial, please be aware of this.
-{: .warning}
-
 > <agenda-title></agenda-title>
 >
 > 1. TOC
@@ -114,15 +103,16 @@ The reports application is included with the Galaxy codebase and this tutorial a
 >    ```diff
 >    --- a/templates/nginx/galaxy.j2
 >    +++ b/templates/nginx/galaxy.j2
->    @@ -103,4 +103,9 @@ server {
+>    @@ -103,4 +103,10 @@ server {
 >     		proxy_set_header Upgrade $http_upgrade;
 >     		proxy_set_header Connection "upgrade";
 >     	}
 >    +
 >    +	location /reports/ {
 >    +		proxy_pass http://{{ galaxy_config.gravity.reports.bind }}:/;
+>    +		proxy_set_header X-Forwarded-Host $host;
+>    +		proxy_set_header X-Forwarded-Proto $scheme;
 >    +	}
->    +
 >     }
 >    {% endraw %}
 >    ```