A note on caching

When making changes to your Lab content, you may notice that updates are not immediate. This is because of caching, which is used to speed up page loading time. There are two levels of caching to keep in mind:

• The Labs Engine caches Lab content forever, unless a request is made with the cache=false parameter. When you are developing your Lab page, use this parameter to see your changes immediately, for example: http://labs.usegalaxy.org.au/?content_root=https://github.com/myusername/myrepo/blob/branch/content/base.yml&cache=false
• Using the cache=false parameter will refresh the cache.
• When making changes to your Lab content, you may notice that updates are not immediate, because GitHub raw content is cached for 5 minutes.
• Caching is automatically disabled if you choose to render locally!

Yes, rendering your lab page locally makes for much faster debugging and polishing! To render your page locally, you will need to install the Galaxy Labs Engine CLI (requires python>=3.10):

        # create a virtual environment
        # (alternatively, you may also wish to use conda for a global environment)
        py -m venv venv
        venv\Scripts\activate

        # install the Labs Engine
        pip install git+https://github.com/usegalaxy-au/galaxy-labs-engine.git

        # Navigate to your content directory
        cd %MY_CONTENT_DIR%

        # serve base.yml in the current directory
        labs-engine serve

        # serve a specific page from the current directory
        labs-engine serve usegalaxy.org.yml

        # upgrade to the latest version (in future)
        pip install --force-reinstall git+https://github.com/usegalaxy-au/galaxy-labs-engine.git
      

        # create a virtual environment
        python -m venv venv
        source venv/bin/activate

        # install the Labs Engine
        pip install git+https://github.com/usegalaxy-au/galaxy-labs-engine.git

        # Navigate to your content directory
        cd $MY_CONTENT_DIR

        # serve base.yml in the current directory
        labs-engine serve

        # serve a specific page from the current directory
        labs-engine serve usegalaxy.org.yml

        # upgrade to the latest version (in future)
        pip install --force-reinstall git+https://github.com/usegalaxy-au/galaxy-labs-engine.git
      

This should start a local development server on http://127.0.0.1:8000. Click the link that appears and your lab page should open in the browser.

Yes - any file/field that accepts markdown can also accept HTML, for example:

• intro.md
• heading_md (in section.yml)

However, be careful about nesting HTML within markdown. Anything inside an HTML element must also be HTML. The following would be invalid:

<p>
  This is a paragraph with a
  [broken link](https://example.com).
</p>

Yes! Using variables is a great way to make a Lab page reuable across Galaxy servers. Variables defined in the base.yml/[server].yml file can be used anywhere that markdown or HTML content is provided. This includes templates like intro.md and also section.yml & *_md values. Any arbitrary variable that you set in the base.yml/[server].yml file can be used in the content:

1. base.yml or [server].yml:

   myvar: foo
   

2. intro.md:

   # Analysis methods
   This is a great place for doing analysis such as {{ myvar }}.
   

3. section_1.yml:

   ...
   – title_md: Can I use variables in my YAML and Markdown/HTML content?
     description_md: |
       Yes, you can use variables like {{ myvar }}.
   

Yes, you can exclude any component in the section schema from specific hosts by listing server names under the exclude_from directive. The server name is just the base name of the [server].yml file. This can be used to exclude items describing server-specific features, such as:

- title_md: How can I increase my storage quota?
  description_md: >
    Please submit a quota request if your Galaxy  account reaches its
    data storage limit. Requests are usually provisioned quickly if you
    provide a reasonable use case for your request.
  exclude_from:
    - usegalaxy.org  # matches the usegalaxy.org.yml content root

Yes, you can use standard Markdown or HTML syntax to include images. When adding the src atrribute to an image tag, you can use relative URLs to specify an image located in your content directory, or an absolute URL to an image hosted elsewhere on the web:

Using Markdown:

![My image description](./static/images/myimage.png)

Using HTML (allows custom styling):

<img src="./static/images/myimage.png" alt="My image description" width="200" height="200">

Or with a full URL (any image available online):

![My image description](https://example.com/myimage.png)

You can list contributors to your Galaxy Lab by adding a CONTRIBUTORS file to your content directory. This file should be a plain-text list of GitHub usernames - one per line. The Labs engine will fetch the user's profile information and display it at the bottom of your Lab Page. If a contributor does not have a GitHub account, you can just add their name.

Standard upload of data to Galaxy, from your computer or from the web.

Before using your sequencing data, it's important to ensure that the data quality is sufficient for your analysis.

Input data:

A haplotype-resolved assembler for PacBio HiFi reads.

Input data:

de novo assembly of single-molecule sequencing reads, designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies.

Input data: