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.*).

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The pipeline creates a 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 table can be used as is (e.g. downloadable tsv file) and/or embedded (e.g. into a 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
2. Pull list of tools relevant to your community from the Galaxy ToolShed
3. Add the list relevant tags for your community in the categories file
4. Review the generated table to curate tools
5. Embed the interactive table in your community page on the Hub
6. Conclusion

Add your community to the Galaxy CoDex

You first need to check if your Community is in the Galaxy CoDex, a central resource for Galaxy communities. If the community is already there, you can move to the next step of this tutorial.

If you community is not already included, follow these steps :

Hands On: Add your community to the Galaxy CoDex

You need to create a new folder in the data/community folder within Galaxy CoDex code source.

1. If not already done, fork the Galaxy Codex repository
2. Go to the 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 + /metadata/categories This will create a folder for your community, a new folder for your community called metadata and a file called categories.
6. Click on Commit changes
7. Fill in the commit message with something like Add X community
8. Click on Create a new branch for this commit and start a pull request
9. Create the pull request by following the instructions

Pull list of tools relevant to your community from the Galaxy ToolShed

To add tools in your community tool table, you will need to indicate a list of tags relevant to your community, and tools associated with this tag will be automatically pulled from the Galaxy ToolShed on a weekly basis. Only tools in the selected ToolShed categories will be added to the filtered table. As a result, it is recommended to include broad categories. You will then be able to remove tools that are not relevant to your community or deprecated.

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 and note the names of these categories
3. Search on the Galaxy ToolShed for some of the popular tools in your community
4. Open the tool entries on the ToolShed, and note their categories

Add the list relevant tags for your community in the categories file

Hands On: Add the ToolShed catgories to the categories file

1. Open or create the file named categories in your comunity metadata folder (communities/<your community>/metadata/categories)

2. Add the name of the categories relevant to your community in the categories file you started above, with 1 ToolShed category per row. For example, see a list of valid ToolShed categories.

   For example:

   Assembly
   Metagenomics
   

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 list of categories to Galaxy CoDex

1. Click on Commit changes at the top
2. Fill in the commit message with something like Add tools categories for my 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.

On the Sunday following the merge of the previous pull request, two files will be generated :

• A JSON file with all tool suites and a short description will be created in communities/<your community>/resources/tools_filtered_by_ts_categories.json.
• A table with all tool suites and a short description will be created in communities/<your community>/metadata/tool_status.tsv.

Review the generated table to curate tools

The generated 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 the file called tools_status.tsv located in communities/<your community>/metadata. The file must include at least 3 columns (with a header):

1. Suite ID
2. To keep indicating whether the tool should be included in the final table (TRUE/FALSE).
3. Deprecated indicating whether the tool is deprecated (TRUE/FALSE).

Example of the tools_status.tsv file:

Suite ID	To keep	Deprecated
abacas	TRUE	FALSE
abricate	TRUE	FALSE
abritamr	TRUE	FALSE

To generate this file, we recommend you to use the generated file tools_status.tsv and to simply update the last two columns.

Hands On: Review tools in your community table

1. Download the tools.tsv file.
2. Open tools.tsv with a Spreadsheet Software.

3. Review each line corresponding to a tool.

   You can also just review some tools.

4. Add TRUE to the To keep column if the tool should be kept, and FALSE if not.
5. Add TRUE or FALSE also to the Deprecated column.
6. Export the new table as TSV.
7. Submit the TSV as tools_status.tsv in your community folder.
8. Wait for the Pull Request to be merged

On the Sunday following the merge of the previous pull request, a curated_tools.tsv file will be generated in communities/<your community>/resources/ folder reflecting the Galaxy tool landscape for your community. You or other community members can review tools in your community from this page to make step-by-step changes or updates to the tools_status.tsv file as needed.

We recommend collaborative work be done with a cloud-based system such as a Google Sheets page.

Here is an overview of the files (the top three files in the table are the most important):

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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 curated resources listing Galaxy tools available for your community, and this table can be embedded in a community page.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• The Galaxy Codex extracts all Galaxy tools to create tables and other resources (yml)

• The tool tables can be filtered by ToolShed categories and community-reviewed lists of tools to keep or exclude

• The generated community Galaxy tools table can be embedded into any website

Frequently Asked Questions

• Topic FAQs
• Galaxy FAQs
• GTN Matrix Chat
• Galaxy Help Forum

Feedback

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Citing this Tutorial

1. Bérénice Batut, Paul Zierep, Solenne Correard, Keiler Collier, Creation of resources listing all the tools and their metadata relevant to your community (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/community/tutorials/community-tool-table/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{community-community-tool-table,
author = "Bérénice Batut and Paul Zierep and Solenne Correard and Keiler Collier",
	title = "Creation of resources listing all the tools and their metadata relevant to your community (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/community/tutorials/community-tool-table/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/community/tutorials/community-tool-table/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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