Creation of an interactive Galaxy tools table for your community

Overview
Creative Commons License: CC-BY Questions:
  • Is it possible to have an overview of all Galaxy tools for a specific scientific domain?

  • How can I create a new overview for a specific Galaxy community or domain?

Objectives:
  • Create a community reviewed table for Galaxy tools within a specific scientific domain

  • Embed an interactive table in a community page

Time estimation: 1 hour
Level: Introductory Introductory
Supporting Materials:
Published: Mar 13, 2024
Last modification: Sep 27, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00426
version Revision: 4

Galaxy offers thousands of tools. They are developed across various GitHub repositories. Furthermore, Galaxy also embraces granular implementation of software tools as sub-modules. In practice, this means that tool suites are separated into Galaxy tools, also known as wrappers, that capture their component operations. Some key examples of suites include Mothur and OpenMS, which translate to tens and even hundreds of Galaxy tools.

While granularity supports the composability of tools into rich domain-specific workflows, this decentralized development and sub-module architecture makes it difficult for Galaxy users to find and reuse tools. It may also result in Galaxy tool developers duplicating efforts by simultaneously wrapping the same software. This is further complicated by a lack of tool metadata, which prevents filtering for all tools in a specific research community or domain, and makes it all but impossible to employ advanced filtering with ontology terms and operations like EDAM ontology.

The final challenge is also an opportunity: the global nature of Galaxy means that it is a big community. Solving the visibility of tools across this ecosystem and the potential benefits are far-reaching for global collaboration on tool and workflow development.

To provide the research community with a comprehensive list of available Galaxy tools, Galaxy Codex was developed to collect Galaxy wrappers from a list of Git repositories and automatically extract their metadata (including Conda version, bio.tools identifiers, and EDAM annotations). The workflow also queries the availability of the tools and usage statistics from the three main Galaxy servers (usegalaxy.*).

A diagram illustrating the Galaxy Codex pipeline, showcasing the various steps involved in creating a community Galaxy tool table.Open image in new tab

Figure 1: Workflow of the Galaxy Codex pipeline. Tool wrappers are parsed from different repositories and additional metadata is retrieved from bio.tools, BioConda, and the main public Galaxy servers. Upon filtering and manual curation of the data for specific scientific communities, the data is transformed into interactive web tables and a tool usage statistic-base word cloud, that can be integrated into any website.

The pipeline creates an interactive table with all tools and their metadata. This table can be filtered to only include tools that are relevant to a specific research community. Here is an example for the microbial related tools:

The generated community-specific interactive table can be used as it and/or embedded, e.g. into the respective Galaxy Hub page or Galaxy subdomain. This table allows further filtering and searching for fine-grained tool selection.

The pipeline is fully automated and executes on a weekly basis. Any research community can apply the pipeline to create a table specific to their community.

The aim is this tutorial is to create such table for a community.

Agenda

In this tutorial, we will cover:

  1. Add your community to the Galaxy Codex pipeline
  2. Review the generated interactive table
    1. Add a tools status list
  3. Embed the interactive table in your community page on the Hub
  4. Conclusion

Add your community to the Galaxy Codex pipeline

To create a table for a community, you first need to create a new folder in the data/community folder within Galaxy Codex code source.

Hands-on: Create a folder for your community
  1. If not already done, fork the Galaxy Codex repository
  2. Go to the data/communities folder
  3. Click on Add file in the drop-down menu at the top
  4. Select Create a new file
  5. Fill in the Name of your file field with: name of your community + /categories

    This will create a new folder for your community and add a categories file to this folder.

One of the filters for the main community table is based on the tool categories on the Galaxy ToolShed. Only tools in the selected ToolShed categories will be added to the filtered table. As a result, it is recommended to include broad categories.

Hands-on: Select the ToolShed categories
  1. Go to the Galaxy ToolShed
  2. On the main page, pick the most obvious categories that represent tools used by your community
  3. Add the name of these categories in the categories file you started above, with 1 ToolShed category per row

    For example:

    Assembly
    Metagenomics
    
  4. Search on the Galaxy ToolShed for some of the popular tools in your community
  5. Open the tool entries on the ToolShed, and note their categories
  6. Add any new categories to the categories file

Once you have a list of the ToolShed categories that you wish to keep, you can submit this to Galaxy Codex.

Hands-on: Submit the new community to Galaxy Codex
  1. Click on Commit changes at the top
  2. Fill in the commit message with something like Add X community
  3. Click on Create a new branch for this commit and start a pull request
  4. Create the pull request by following the instructions

The Pull Request will be reviewed. Make sure to respond to any feedback.

Once the Pull Request is merged, the interactive table will be created and made available online at https://galaxyproject.github.io/galaxy_codex/<your community>.

Review the generated interactive table

The interactive table will contain all the tools associated with the ToolShed categories that you selected. However, not all of these tools might be interesting for your community.

Galaxy Codex allows for an additional optional filter for tools, that can be defined by the community curator (maybe that is you !).

The additional filter must be stored in a file called tools_status.tsv located in data/community/<your community>. The file must include 3 columns (without header):

  1. The Galaxy wrapper id corresponding to the IDs in the tools.tsv file in results/<your community>.
  2. Whether the tool should be included in the final table (TRUE/FALSE).
  3. Whether the tool is deprecated (TRUE/FALSE).

Example of the tools_status.tsv file:

abacas	TRUE	FALSE
abricate	TRUE	FALSE
abritamr	TRUE	FALSE

Have a look on the microGalaxy tool stats TSV for an example of the file that is used to manually filter the tools for a community.

Add a tools status list

Hands-on: Review tools in your community table
  1. Download the tools.tsv file in results/<your community>.
  2. Open tools.tsv with a Spreadsheet Software.
  3. Review each line corresponding to a tool

    You can also just review some tools. Those tools that are not reviewed will be have FALSE in the Reviewed columns the updated table.

    1. Change the value in the Reviewed column from FALSE to TRUE (this will be done automatically if an entry of the tool in tools_status.tsv exists).
    2. Add TRUE to the To keep column if the tool should be kept, and FALSE if not.
    3. Add TRUE or FALSE also to the Deprecated column.
  4. Copy paste the Galaxy wrapper id, To keep, Deprecated column in a new table (in that order).

    This can also be done using the reference function of your Spreadsheet Software.

  5. Export the new table as TSV (without header).
  6. Submit the TSV as tools_status.tsv in your community folder.
  7. Wait for the Pull Request to be merged

You should have now an interactive table reflecting the Galaxy tool landscape for your community. You can step-by-step review all tools in your community and update the tools_status.tsv file. You could also share this file with your community members and discuss weather the tool should be kept or not. Collaborative work could be established using google spreadsheet.

Embed the interactive table in your community page on the Hub

The interactive table you have created can be embedded in your community page on the Hub, e.g. microGalaxy.

Hands-on: Embed your table as an iframe
  1. If not already done, fork the repository Galaxy Hub
  2. Open or create your community page: content/community/sig/<your community>/index.md
  3. Add an iframe to embed the interactive table

    <iframe
      id="inlineFrameExample"
      title="Microbial related tools"
      width="100%"
      height="600"
      frameBorder="0"
      src="https://galaxyproject.github.io/galaxy_codex/<your_community>/">
    </iframe>
    
  4. Replace <your_community> by the name of your community in src
  5. Submit the changes
  6. Wait for the Pull Request to be merged

Conclusion

You now have an interactive table with Galaxy tools available for your community, and this table is embedded in a community page.