join-session.qmd

# Join the Training Session {#sec-join-session}

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## Use this link to join the training session

- [{{< var galaxy.session >}}]({{< var galaxy.session >}})

Galaxy EU have deployed a dedicated cloud service just for this workshop to use[^1]. No-one outside of our workshop has access to this machine, and all of the jobs in our training session will run on this server Use the link above and log in with your `usegalaxy.eu` account (instructions to set up this account can be found in @sec-galaxy-registration).

[^1]: This is a single server with 120 cores and 205 GB of RAM.
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## The Galaxy workspace layout

Once you have joined the session, you will see the Galaxy workspace, which should look similar to @fig-galaxy-workspace. There are three sections to the workspace: the `Tools` sidebar, the `History/Workflow` sidebar, and the central `Workspace` area. You will become more familiar with these as you move through the workshop.

![An empty Galaxy workspace. The workspace is divided into three sections. On the left is the `Tools` sidebar, which presents the software tools available on the current Galaxy instance. On the right is the `History` or `Workflow` sidebar, which describes the data and steps being used in the current Galaxy workflow. The largest section, in the centre, shows details of a selected tool including options to set or change parameters, or the contents of the dataset, depending what is selected from the `History` sidebar.](assets/images/galaxy_landing.png){#fig-galaxy-workspace fig-alt="Screen capture of a Galaxy workspace, with the three sections 'Tools,' 'Workspace,' and 'History/Workflow' indicated." width=80%}

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## The `Tools` sidebar

The `Tools` sidebar on the left of the window initially presents all the tools available on the Galaxy instance being used. These are grouped into sections by the kind of task they can be used for, such as manipulating text, or assembling sequenced reads.

This sidebar also provides useful links, such as for uploading your own data to the Galaxy instance (`Upload Data`), and for importing data from public databases, like [Ensembl](https://www.ensembl.org/index.html). There is also a search field at the top of the sidebar which initially contains the text `search tools`. You can enter the name of a tool or action into this field, and the sidebar will present the matching software on the Galaxy instance.
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## The `History/Workflow` sidebar

The `History/Workflow` sidebar at the right of the window will initially be empty. As you work through the exercises this sidebar will become populated with your data, the actions you take on the data, and the results of those actions. The `History` will have no name specified, so you should see the placeholder `Unnamed history`, and the text `This history is empty`.

When you log into a Galaxy instance that you have used before, you may see the most recent history/workflow that you used, and you may have options for loading previous histories/workflows into the current workspace.
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## The `Workspace`

The largest, central region of the window is the `Workspace`. This is an area that presents several kinds of information. Depending on context, it may provide information about the Galaxy instance, present datasets (or summaries/visualisations of datasets), or ways to interact with the individual tools that you will use.

::: {#fig-workspaces layout-nrow=2 fig-alt="Four images of the Galaxy workspace showing its use in a range of contexts: news and information, inspecting a dataset, interactive visualisation of results, and setting parameters for analysis."}

![News and information](assets/images/workspace_galaxy_info.png){#fig-workspace-news}

![Inspecting data](assets/images/workspace_data.png){#fig-workspace-data}

![Interactive visualisations](assets/images/workspace_data_visualisation.png){#fig-workspace-datavis}

![Setting parameters for software and analyses](assets/images/workspace_tool_settings.png){#fig-workspace-software}

Four uses of the `Workspace` area in Galaxy.

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## Give A Name To The History

It is helpful to give the workflow/history that you work with a name. This will help you find it again when you reuse the Galaxy EU instance.

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- When you name a workflow, give it a concise title that expresses the purpose of the workflow.
- You can also add annotation that describes the workflow and provides more information than the name alone conveys.
- You can rename or re-annotate your workflow at any time.
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To assign a name to your workflow:

1. Click on the pen icon next to `Unnamed history`
2. Enter a name for the workflow in the top `Unnamed history` field
3. Enter additional text describing the workflow in the lower `Annotation (optional)` field
4. Click the `Save` button.

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## Video: Renaming A Galaxy Workflow
{{< video assets/movies/galaxy-01-rename-history.mp4 title="Renaming your Galaxy history" >}}
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