GALAXY LAB PAGES
Welcome to the Galaxy Labs Engine! This endpoint is used to generate "exported" Galaxy Lab landing pages from remote content hosted on GitHub. You can use this endpoint to rapidly create your own Galaxy Lab pages by pointing to your own remote content.
- See the content used to generate this documentation page here.
- See a full working example of an exported Galaxy Lab page here.
- See a minimal working example of a lab page here.
This custom introductory text was pulled down from GitHub and rendered in real time. Updates to this text on the remote will be reflected on this page. Note that GitHub raw content is cached for 300 seconds, so some updates may take a few minutes to appear on this page.
- The root of your site's content should be a YAML file - see base.yml for the content root of this page.
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Request your page by pointing to your remote content with the
content_rootGET parameter (take a look at URL for this page). For example, we can explicitly request this page with:
http://labs.usegalaxy.org.au/?content_root=https://raw.githubusercontent.com/usegalaxy-au/galaxy-labs-engine/refs/heads/main/app/labs/static/labs/content/docs/base.yml - The web server will fetch your content from GitHub (or anywhere on the internet) and render it into this page.
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Note that
base.ymlpoints to other files (YAML, HTML, CSS and images), which are located in the same remote directory (e.g. on GitHub). You can template the entire page with these files! -
The most useful part of this machinery is the
sectionscontent, which populates the tool/workflow sections below. See section_1.yml and section_2.yml for examples of how to structure this content in YAML format.
- Copy our example content directory to your own github repository.
- Build your Galaxy Lab's info, tools and workflows by editing the YAML and HTML files. Custom CSS and JavaScript are possible too.
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Request the site with the
content_rootGET parameter pointing to your remote content:
http://labs.usegalaxy.org.au/?content_root=https://github.com/myusername/myrepo/blob/branch/content/base.yml
A note on caching
When making changes to your Lab content, you may notice that updates are not immediate. This is because of caching. There are two levels of caching to keep in mind:
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The Labs Engine caches Lab content forever, unless a request is made with the
cache=falseparameter. 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=falseparameter will refresh the cache. This happens automatically on every pull request to the Galaxy Codex repository, where global Labs content is stored. - When making changes to your Lab content, you may notice that updates are not immediate, because GitHub raw content is cached for 5 minutes.
The webpage includes Bootstrap 5.1, Material icons, and FontAwesome 5.15 and JQuery 3.6 so you can use any styling/functionality defined there. This means you can have webforms, interactive elements, and more. Check out Galaxy Australia's Genome Lab conclusion for an example of more complex usage including modals and webforms. Modals (popups) are a great way to hide additional information until the user requests it. Try one now!
Example section
Common tools are listed here, or search for more in the full tool panel to the left.
A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below. Learn more.
You can upload your data to Galaxy using the Upload tool from anywhere in Galaxy. Just look for the "Upload data" button at the top of the tool panel.
We recommend subsampling large data sets to test tools and workflows.
A useful tool is seqtk_seq, setting the parameter at "Sample fraction of sequences".
Example section with subsections
The tools in this section have been divided into subsections to make it
easier for users to find the tools they need. This must replace the
entire value of the content key i.e. you can't mix
subsections with standalone items.
This is my first subsection
Another subsection
A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below. Learn more .
Assembly with PacBio HiFi data
This How-to-Guide will describe the steps required to assemble your genome on the Galaxy Australia platform, using multiple workflows.
Assembly with Nanopore data and polishing with Illumina data
This tutorial describes the steps required to assemble a genome on Galaxy with Nanopore and Illumina data
Yes. Galaxy Australia has assembly tools for small prokaryote genomes as well as larger eukaryote genomes. We are continually adding new tools and optimising them for large genome assemblies - this means adding enough computer processing power to run data-intensive tools, as well as configuring aspects such as parallelisation
Please contact us if:
- you need to increase your data storage limit
- there is a tool you wish to request
- a tool appears to be broken or running slowly
- See the tutorials in this Help section. They cover different approaches to genome assembly
- Read the methods in scientific papers about genome assembly, particularly those about genomes with similar characteristics to those in your project
- See the Workflows section for examples of different approaches to genome assembly - these cover different sequencing data types, and a variety of tools.
Contributors
