Merge branch 'galaxyproject:main' into DASH-1256

galaxyproject · Oct 24, 2023 · 3eb0438 · 3eb0438
2 parents cca4600 + e875bc1
commit 3eb0438
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diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -1566,6 +1566,10 @@ sylviamahara:
     github: false
     joined: 2022-03
 
+tb143:
+    name: Tim Beck
+    joined: 2023-09
+
 tduigou:
     name: Thomas Duigou
     email: [email protected]
@@ -1742,6 +1746,17 @@ yvanlebras:
     elixir_node: fr
 
 
+paulzierep:
+    name: Paul Zierep
+    email: [email protected]
+    orcid: 0000-0003-2982-388X
+    joined: 2023-02
+
+SNG888:
+    name: Sandra Ng
+    email: [email protected]
+    joined: 2023-07
+
 # Funders / External Entities
 carpentries:
     name: The Carpentries
@@ -1896,3 +1911,15 @@ biont:
     funding_system: cordis
     funding_statement: |
       Co-funded by the European Union
+
+
+ELIXIR-UK-DaSH:
+    name: DASH UK
+    joined: 2023-10
+    avatar: "https://github.com/galaxyproject/training-material/blob/main/shared/images/dash.png?raw=true"
+    url: https://elixiruknode.org/projects/elixir-uk-dash/
+    funder: true
+    funding_system: ukri
+    funding_id: MR/V038966/1
+    funding_statement: |
+      This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.
diff --git a/shared/images/dash.png b/shared/images/dash.png
diff --git a/shared/images/ukri.png b/shared/images/ukri.png
diff --git a/topics/admin/tutorials/apptainer/tutorial.md b/topics/admin/tutorials/apptainer/tutorial.md
@@ -185,7 +185,7 @@ Now, we will configure Galaxy to run tools using Apptainer containers, which wil
 >         tool_data_table_config_path: /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml
 >    +    # Tool Dependencies
 >    +    dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml"
->    +    containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
+>    +    container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
 >       gravity:
 >         process_manager: systemd
 >         galaxy_root: "{{ galaxy_root }}/server"
@@ -195,7 +195,7 @@ Now, we will configure Galaxy to run tools using Apptainer containers, which wil
 >     
 >    +galaxy_config_templates:
 >    +  - src: templates/galaxy/config/container_resolvers_conf.yml.j2
->    +    dest: "{{ galaxy_config.galaxy.containers_resolvers_config_file }}"
+>    +    dest: "{{ galaxy_config.galaxy.container_resolvers_config_file }}"
 >    +  - src: templates/galaxy/config/dependency_resolvers_conf.xml
 >    +    dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"
 >    +
@@ -393,14 +393,14 @@ After finishing the CVMFS tutorial, come back, and do this hands-on.
 
 > <hands-on-title>Optional: Configure Galaxy to use Apptainer containers from CVMFS</hands-on-title>
 >
-> 1. Edit the `group_vars/galaxyservers.yml` file and add `containers_resolvers_config_file` and `galaxy_singularity_images_cvmfs_path`:
+> 1. Edit the `group_vars/galaxyservers.yml` file and add `container_resolvers_config_file` and `galaxy_singularity_images_cvmfs_path`:
 >    {% raw %}
 >    ```yaml
 >    galaxy_singularity_images_cvmfs_path: "/cvmfs/singularity.galaxyproject.org/all/"
 >    galaxy_config:
 >      galaxy:
 >        ...
->        containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
+>        container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
 >    ```
 >    {% endraw %}
 >

diff --git a/topics/admin/tutorials/data-library/tutorial.md b/topics/admin/tutorials/data-library/tutorial.md
@@ -87,7 +87,7 @@ Before we can import local data, we need to configure Galaxy to permit this. Add
 >    @@ -88,6 +88,9 @@ galaxy_config:
 >         # Tool Dependencies
 >         dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml"
->         containers_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
+>         container_resolvers_config_file: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
 >    +    # Data Library Directories
 >    +    library_import_dir: /libraries/admin
 >    +    user_library_import_dir: /libraries/user

diff --git a/topics/admin/tutorials/job-destinations/tutorial.md b/topics/admin/tutorials/job-destinations/tutorial.md
@@ -652,7 +652,7 @@ Such form elements can be added to tools without modifying each tool's configura
 >         slow_query_log_threshold: 5
 >         enable_per_request_sql_debugging: true
 >    @@ -137,6 +146,8 @@ galaxy_config_templates:
->         dest: "{{ galaxy_config.galaxy.containers_resolvers_config_file }}"
+>         dest: "{{ galaxy_config.galaxy.container_resolvers_config_file }}"
 >       - src: templates/galaxy/config/dependency_resolvers_conf.xml
 >         dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"
 >    +  - src: templates/galaxy/config/job_resource_params_conf.xml.j2

diff --git a/topics/fair/images/CLUSTER_Zenodo.png b/topics/fair/images/CLUSTER_Zenodo.png
diff --git a/topics/fair/images/DataAccessProcess.png b/topics/fair/images/DataAccessProcess.png
diff --git a/topics/fair/images/DataCat.png b/topics/fair/images/DataCat.png
diff --git a/topics/fair/images/DataDictSolution.png b/topics/fair/images/DataDictSolution.png
diff --git a/topics/fair/images/DataDictionaryHandsOn.png b/topics/fair/images/DataDictionaryHandsOn.png
diff --git a/topics/fair/images/Datesremoved.png b/topics/fair/images/Datesremoved.png
diff --git a/topics/fair/images/ExampleDataDict1.png b/topics/fair/images/ExampleDataDict1.png
diff --git a/topics/fair/images/Patient_data.png b/topics/fair/images/Patient_data.png
diff --git a/topics/fair/images/Patient_dates.png b/topics/fair/images/Patient_dates.png
diff --git a/topics/fair/images/RAMAP_graphic.png b/topics/fair/images/RAMAP_graphic.png
diff --git a/topics/fair/tutorials/bioimage-REMBI/tutorial.md b/topics/fair/tutorials/bioimage-REMBI/tutorial.md
@@ -32,7 +32,8 @@ contributions:
     - Laura190
     - kkamieniecka
     - poterlowicz-lab
-
+  funding:
+      - ELIXIR-UK-DaSH
 subtopic: fair-data
 
 requirements:

diff --git a/topics/fair/tutorials/bioimage-metadata/tutorial.md b/topics/fair/tutorials/bioimage-metadata/tutorial.md
@@ -34,7 +34,8 @@ contributions:
     - Laura190
     - kkamieniecka
     - poterlowicz-lab
-
+  funding:
+      - ELIXIR-UK-DaSH
 subtopic: fair-data
 
 requirements:

diff --git a/topics/fair/tutorials/data-management/tutorial.md b/topics/fair/tutorials/data-management/tutorial.md
@@ -27,6 +27,8 @@ contributions:
     - poterlowicz-lab
   editing:
     - hexylena
+  funding:
+      - ELIXIR-UK-DaSH
 subtopic: fair-data
 
 requirements:

diff --git a/topics/fair/tutorials/fair-clinical/faqs/index.md b/topics/fair/tutorials/fair-clinical/faqs/index.md
@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---
diff --git a/topics/fair/tutorials/fair-clinical/tutorial.bib b/topics/fair/tutorials/fair-clinical/tutorial.bib
@@ -0,0 +1,11 @@
+@article{wilkinson,
+  title={The FAIR Guiding Principles for scientific data management and stewardship},
+  author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
+  journal={Scientific data},
+  doi = {10.1038/sdata.2016.18},
+  volume={3},
+  number={1},
+  pages={1--9},
+  year={2016},
+  publisher={Nature Publishing Group}
+}