diff --git a/topics/fair/tutorials/ro-crate-in-galaxy/images/show_invocation.png b/topics/fair/tutorials/ro-crate-in-galaxy/images/show_invocation.png new file mode 100644 index 00000000000000..25107bf01adea1 Binary files /dev/null and b/topics/fair/tutorials/ro-crate-in-galaxy/images/show_invocation.png differ diff --git a/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-export.png b/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-export.png index da03cbeb1a4bde..6c79ab35135f26 100644 Binary files a/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-export.png and b/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-export.png differ diff --git a/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-summary.png b/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-summary.png index dc731a46e0c46c..013b3485e54036 100644 Binary files a/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-summary.png and b/topics/fair/tutorials/ro-crate-in-galaxy/images/workflow-invocation-summary.png differ diff --git a/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.md b/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.md index 9a4d38d478b49c..f3a2a02fa48d0d 100644 --- a/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.md +++ b/topics/fair/tutorials/ro-crate-in-galaxy/tutorial.md @@ -20,6 +20,8 @@ priority: 2 contributions: authorship: - pauldg + editing: + - Marie59 funding: - by-covid - eurosciencegateway @@ -81,25 +83,27 @@ Let’s run the workflow and export the RO-Crate. > https://zenodo.org/record/1319069/files/iris.csv > ``` > -> Tip: Importing via links: -> -> - Copy the link location -> - Open the Galaxy Upload Manager (galaxy-upload on the top-right of the tool panel) -> - Select Paste/Fetch Data -> - Paste the link(s) into the text field -> - Press Start -> - Close the window +> > Importing via links +> > +> > - Copy the link location +> > - Open the Galaxy Upload Manager (galaxy-upload on the top-right of the tool panel) +> > - Select Paste/Fetch Data +> > - Paste the link(s) into the text field +> > - Press Start +> > - Close the window +> {: .tip} > > 2. Run **GTN Training: Galaxy 101 For Everyone** workflow using the following parameters: > - *"Send results to a new history"*: `No` > - *"1: Iris Dataset""*: the `iris.csv` file we just uploaded > -> Tip: Running a workflow: -> - Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows. -> - Click on the workflow-run (Run workflow) button next to your workflow -> - Configure the workflow as needed -> - Click the Run Workflow button at the top-right of the screen -> - You may have to refresh your history to see the queued jobs +> > Running a workflow +> > - Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows. +> > - Click on the {% icon workflow-run %} (Run workflow) button into your workflow box +> > - Configure the workflow as needed +> > - Click the {% icon workflow-run %} Run Workflow button at the top-right of the screen +> > - You may have to refresh your history to see the queued jobs +> {: .tip} > > 3. **View the workflow outputs** once the workflow has completed > - The workflow produces several text and tabular outputs, and two plot (image) outputs @@ -108,11 +112,13 @@ Let’s run the workflow and export the RO-Crate. ## Export the Workflow Run Crate -After the workflow has completed, we can export the RO-Crate. The crate does not appear in your history, but can be accessed from the **User -> Workflow Invocations** menu on the top bar. +After the workflow has completed, we can export the RO-Crate. The crate does not appear in your history, but can be accessed from the {% icon galaxy-history-options %} **-> Show Invocations** menu on the top right of your history OR on the left pannel from the {% icon galaxy-panelview %} Workflow Invocations . > Export the Workflow Run Crate > -> 1. In the top menu bar, go to **User -> Workflow Invocations** +> 1. In the top right of your history, go to {% icon galaxy-history-options %} **-> Show Invocations** +> +> ![screenshot of the history options to get the Show invocations button](./images/show_invocation.png) > > 2. Our latest workflow run should be listed at the top. > - Click on it to expand it: @@ -121,11 +127,12 @@ After the workflow has completed, we can export the RO-Crate. The crate does not > > 3. Click on the **Export** tab in the expanded view of the workflow invocation. > -> 4. You should see a page like this. It contains: -> - The different export options -> - Location where the export should be sent to (Download locally or a remote location) -> -> 5. Click on the Download option +> 4. Click on the Export tab in the expanded view of the workflow invocation. +> You should see a page that contains three download options: +> - Research Object Crate (RO-Crate) +> - BioCompute Object +> - File +> 5. Click on the **Generate** {% icon galaxy-download %} option of the RO-Crate box (1st box) > > ![screenshot of the beginning of the workflow run export options](./images/workflow-invocation-export.png) >