galaxyproject · shiltemann · Nov 27, 2023 · Oct 6, 2023 · Oct 6, 2023 · Oct 9, 2023
diff --git a/_config.yml b/_config.yml
@@ -92,6 +92,7 @@ icon-tag:
   cofest: fas fa-users
   comment: far fa-comment-dots
   congratulations: far fa-thumbs-up
+  copy: far fa-copy
   curriculum: fas fa-graduation-cap
   details: fas fa-info-circle
   docker_image: fab fa-docker

@@ -79,9 +79,9 @@ def figurify(page, site)
           image = insert_image(url, alt, style, dimensions, actual_path)
 
           %(
-            <figure id="figure-#{num_figure}" style="max-width: 90%; margin:auto;">
+            <figure id="figure-#{num_figure}" style="max-width: 90%;">
               #{image}
-              <a target="_blank" href="#{url}" rel="noopener noreferrer"><small>Open image in new tab</small></a>
+              <a target="_blank" href="#{url}" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/>
               <figcaption>
                 <span class="figcaption-prefix"><strong>#{prefix}#{num_figure}</strong>:</span> #{title}
               </figcaption>

@@ -362,7 +362,9 @@ div.main-content {
 
 figure {
   text-align: center;
-  margin: 1rem 2rem;
+  margin: 2rem;
+  border: thin silver solid;
+  padding: 1rem;
 
   & > img {
       margin-bottom: 1rem;
@@ -374,6 +376,11 @@ figure {
   }
 }
 
+@media (max-width:992px) {
+  figure {
+  margin: 1rem;
+ }
+}
 
 :not(pre) > code {
     color: var(--code-foreground);
@@ -1665,7 +1672,7 @@ figure > a[target="_blank"]::after {
 	justify-content: space-between;
 	align-items: flex-end;
 	row-gap: 1em;
-	
+
 	figure {
 		max-width: 20em;
 		margin: 0rem 0.5rem;

diff --git a/faqs/galaxy/collections_build_list.md b/faqs/galaxy/collections_build_list.md
@@ -15,3 +15,5 @@ contributors: [shiltemann, hexylena]
 * Enter a name for your collection
 * Click **Create List** to build your collection
 * Click on the checkmark icon at the top of your history again
+
+![Creating a simple collection]({{site.baseurl}}/faqs/galaxy/images/create_simple_list.png "Creating a simple (list) collection in Galaxy's history")
diff --git a/faqs/galaxy/datasets_upload_from_genomeark.md b/faqs/galaxy/datasets_upload_from_genomeark.md
@@ -0,0 +1,13 @@
+---
+title: Upload datasets from GenomeArk
+area: data upload
+box_type: tip
+layout: faq
+contributors: [nekrut]
+---
+
+1. Open the file {% icon galaxy-upload %} __upload__ menu
+2. Click on **Choose remote files** tab
+3. Click on the **Genome Ark** button and then click on **species**
+
+You can find the data by following this path: `/species/${Genus}_${species}/${specimen_code}/genomic_data`. Inside a given datatype directory (*e.g.* `pacbio`), select all the relevant files individually until all the desired files are highlighted and click the <kbd>Ok</kbd> button. Note that there may be multiple pages of files listed. Also note that you may not want every file listed.
diff --git a/faqs/galaxy/images/create_simple_list.png b/faqs/galaxy/images/create_simple_list.png
diff --git a/faqs/galaxy/images/upload_fasta_via_url.png b/faqs/galaxy/images/upload_fasta_via_url.png
diff --git a/faqs/galaxy/images/upload_fastqsanger_via_url.png b/faqs/galaxy/images/upload_fastqsanger_via_url.png
diff --git a/faqs/galaxy/workflows_import.md b/faqs/galaxy/workflows_import.md
@@ -12,3 +12,8 @@
   - Option 1: Paste the URL of the workflow into the box labelled *"Archived Workflow URL"*
   - Option 2: Upload the workflow file in the box labelled *"Archived Workflow File"*
 - Click the **Import workflow** button
+
+Below is a short video demonstrating how to import a workflow from GitHub using this procedure:
+
+<p align="center"><iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/hoP36Te5wko" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe></p>
+
diff --git a/faqs/galaxy/workflows_import_from_dockstore.md b/faqs/galaxy/workflows_import_from_dockstore.md
@@ -0,0 +1,26 @@
+---
+title: Import workflows from DockStore
+area: workflows
+box_type: tip
+layout: faq
+contributors: [nekrut]
+---
+
+[Dockstore](https://dockstore.org/) is a free and open source platform for sharing reusable and scalable analytical tools and workflows.
+
+1. Go to [DockStore](https://dockstore.org).
+2. Select any Galaxy workflow you want to import.
+3. Click on "Galaxy" dropdown within the "Launch with" panel located in the upper right corner.
+4. Select a galaxy instance you want to launch this workflow with.
+5. You will be redirected to Galaxy and presented with a list of workflow versions.
+6. Click the version you want (usually the latest labelled as "main")
+7. You are done!
+
+> <warning-title>Make sure you are logged in!</warning-title>
+> Ensure that you are logged in into your Galaxy account!
+{: .warning}
+
+The following short video walks you through this uncomplicated procedure:
+
+<p align="center"><iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/K2wFrSLFpa0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe></p>
+{: .hands_on}
diff --git a/faqs/galaxy/workflows_import_from_workflowhub.md b/faqs/galaxy/workflows_import_from_workflowhub.md
@@ -3,21 +3,25 @@
 area: workflows
 box_type: tip
 layout: faq
-contributors: [gallardoalba, abueg]
+contributors: [gallardoalba, abueg, nekrut]
 ---
 
 [WorkflowHub](https://workflowhub.eu/) is a workflow management system which allows workflows to be FAIR (Findable, Accessible, Interoperable, and Reusable), citable, have managed metadata profiles, and be openly available for review and analytics.
 
-> <hands-on-title> Import a workflow </hands-on-title>
->
-> 1. Click on the **Workflow** menu, located in the top bar.
-> 2. Click on the **Import** button, located in the right corner.
-> 3. In the section "Import a Workflow from Configured GA4GH Tool Registry Servers (e.g. Dockstore)", click on **Search form**.
->
-> 4. In the **TRS Server: *workflowhub.eu*** menu you should type {% if include.filter %}`{{ include.filter }}`{% else %}your query.{% endif %}
->    ![galaxy TRS workflow search field, name:vgp is entered in the search bar, and five different workflows all labelled VGP are listed]({% link topics/assembly/images/vgp_assembly/workflow_list.png %})
-> 5. Click on the desired workflow, and finally select the latest available version.
-{: .hands_on}
+> <warning-title>Make sure you are logged in!</warning-title>
+> Ensure that you are logged in into your Galaxy account!
+{: .warning}
+
+1. Click on the **Workflow** menu, located in the top bar.
+2. Click on the **Import** button, located in the right corner.
+3. In the section "Import a Workflow from Configured GA4GH Tool Registry Servers (e.g. Dockstore)", click on **Search form**.
+4. In the **TRS Server: *workflowhub.eu*** menu you should type {% if include.filter %}`{{ include.filter }}`{% else %}your query.{% endif %}
+   ![galaxy TRS workflow search field, name:vgp is entered in the search bar, and five different workflows all labelled VGP are listed]({% link topics/assembly/images/vgp_assembly/workflow_list.png %})
+5. Click on the desired workflow, and finally select the latest available version.
 
+After that, the imported workflows will appear in the main workflow menu. In order to run the workflow, just need to click in the {% icon workflow-run %} **Run workflow** icon.
 
-After that, the imported workflows will appear in the main workflow menu. In order to initialize the workflow, we just need to click in the {% icon workflow-run %} **Run workflow** icon.
+Below is a short video showing this uncomplicated procedure:
+
+<p align="center"><iframe width="560" height="315" src="https://www.youtube-nocookie.com/embed/hoP36Te5wko" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe></p>
+{: .hands_on}
@@ -0,0 +1,13 @@
+---
+title: Upload fasta datasets via links
+area: data upload
+box_type: tip
+layout: faq
+contributors: [nekrut]
+---
+
+Uploading `fasta` or `fasta.gz` datasets via URL.
+
+![UploadAnimatedPng]({{site.baseurl}}/faqs/galaxy/images/upload_fasta_via_url.png)
+
+
@@ -6,6 +6,7 @@ layout: faq
 contributors: [nekrut]
 ---
 
+Uploading `fastqsanger` or `fastqsanger.gz` datasets via URL.
 
 1. Click on **Upload Data** on the top of the left panel:
 
@@ -24,3 +25,10 @@ contributors: [nekrut]
 	![ChangeTypeDropDown]({{site.baseurl}}/faqs/galaxy/images/paste_fetch_set_data_type.png):
 
 
+> <warning-title>Danger: Make sure you choose corect format!</warning-title>
+> When selecting datatype in "**Type (set all)**" dropdown, make sure you select `fastaqsanger` or `fastqsanger.gz` BUT NOT `fastqcssanger` or anything else!
+{: .warning}
+
+![UploadAnimatedPng]({{site.baseurl}}/faqs/galaxy/images/upload_fastqsanger_via_url.png)
+
+