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资源说明：:microscope::books: Galaxy Tool wrappers
[](https://travis-ci.org/bgruening/galaxytools) [](https://zenodo.org/badge/latestdoi/5466/bgruening/galaxytools) Galaxy Tool wrappers ==================== This repository contains a variety of different tools that can be installed and used inside the Galaxy. Many tools are already included in the [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/), others needs some more [love](https://github.com/bgruening/galaxytools/issues). Wrapping tools for use in Galaxy is easy! If you want to start please see the [Galaxy wiki](https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial) or get in contact. If you want to contribute to this repository please see our [contributing guidelines](CONTRIBUTING.md) and our list of [issues](https://github.com/bgruening/galaxytools/issues). Highlights ---------- * [ChemicalToolBox](./chemicaltoolbox) includes a lot of cheminformatic tools into Galaxy * [RNA tools](./tools/rna_tools) are integrated as part of the [de.NBI](http://www.denbi.de) RNA Bioinformatics Center * Genome Annotation tools Other repositories with high quality tools ------------------------------------------ * [IUC repo](https://github.com/galaxyproject/tools-iuc) * [DevTeam repo](https://github.com/galaxyproject/tools-devteam) * [Peter Cock's blast repo](https://github.com/peterjc/galaxy_blast) * [Peter Cock's pico_galaxy repo](https://github.com/peterjc/pico_galaxy) * [Biopython repo](https://github.com/biopython/galaxy_packages) * [Galaxy Proteomics repo](https://github.com/galaxyproteomics/tools-galaxyp) Running the tests ==================== First, install Planemo. Run the commands at the project root directory. ``` python3 -m venv planemo . planemo/bin/activate pip install planemo ``` To run the tests for a specific tool (e.g., pca) in a specific folder (e.g. sklearn) ``` planemo test --docker tools/sklearn/pca.xml ``` To run the tests for all tools in a specific folder (e.g. sklearn) ``` planemo test --docker tools/sklearn ``` To run the tests for all tools in all folders ``` planemo test --docker tools ``` 3 steps to get your tool into Galaxy - A real-world example ============================================================== In this blog post, we will explain how you can get your software tool into a Galaxy server and with this, exposed to thousands of researchers. For this purpose, we will follow David’s steps to add the very generic UNIX `diff` tool to Galaxy. The first step to getting your software tool deployed into a Galaxy instance is to develop a Conda package for it. Conda is the *de facto* standard in many different communities to deploy software easily and reproducibly. The European Galaxy team is heavily involved in the [conda-forge](https://conda-forge.org) and [Bioconda](https://www.nature.com/articles/s41592-018-0046-7) projects and Galaxy does have built-in support for both channels. If your software tool is from the Biomedical domain, we recommend the Bioconda channel. Otherwise, create a Conda package for conda-forge. Here, David has created the following [Pull Request (PR) against the conda-forge repo](https://github.com/conda-forge/staged-recipes/pull/11170): **Step 1 - the Conda package**: [https://github.com/conda-forge/staged-recipes/pull/11170](https://github.com/conda-forge/staged-recipes/pull/11170) After merging, a [diffutils repository](https://github.com/conda-forge/diffutils-feedstock) is created and the [Conda package](https://anaconda.org/conda-forge/diffutils) is available usually within 30 min. The second step is to create the Galaxy wrapper. A Galaxy wrapper is a formal description of all inputs, outputs and parameters of your tool, so that Galaxy can generate a GUI out of it and later a command to send to the cluster. You will find a tutorial on how to create such a wrapper in the [planemo](https://planemo.readthedocs.io/en/latest/writing.html) documentation. The community has created a few best-practices for [Galaxy wrapper development](https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html) and we recommend to follow them as this will ensure your tools are high-quality and can be deployed at the big public Galaxy servers. David has created the following PR was created against a public repository that collects a variety of different tools. **Step 2 - the Galaxy wrapper**: [https://github.com/bgruening/galaxytools/pull/966](https://github.com/bgruening/galaxytools/pull/966) We recommend the submission of your tool to one of the bigger community projects like the ones listed below. This has the advantage that you will most likely get a review and can improve your tool, but also get some infrastructure for automated testing and ToolShed deployment for free. Other repositories with Galaxy tools: * [IUC repo](https://github.com/galaxyproject/tools-iuc) * [Björn Grüning's repo](https://github.com/bgruening/galaxytools) * Peter Cock's repos: * [blast repo](https://github.com/peterjc/galaxy_blast) * [pico repo](https://github.com/peterjc/pico_galaxy) * [mira repo](https://github.com/peterjc/galaxy_mira) * [Metabolomics](https://github.com/workflow4metabolomics/tools-metabolomics) * [Proteomics](https://github.com/galaxyproteomics/tools-galaxyp) * [Colibread Galaxy Tools](https://github.com/genouest/tools-colibread) * [Greg von Kuster's repo](https://github.com/gregvonkuster/galaxy-csg) * [EI repo](https://github.com/TGAC/earlham-galaxytools) * [AAFC-MBB Canada repo](https://github.com/AAFC-MBB/Galaxy/tree/master/wrappers) * [Mark Einon's repo](https://gitlab.com/einonm/galaxy-tools) * [National Microbiology Laboratory's repo](https://github.com/phac-nml/galaxy_tools) Once David’s Galaxy wrapper PR passed all tests and was merged, it was automatically pushed to the [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/view/bgruening/diff/), an app store for Galaxy. From there, every Galaxy instance can install tools (apps). Furthermore, a bot is automatically creating [(Bio)Containers](https://biocontainers.pro) (Docker, rkt and Singularity) by tracking all Galaxy tools to ensure that a container exists for each tool. You can see the bot in action in the following PR: Automatic containers: [https://github.com/BioContainers/multi-package-containers/pull/1236](https://github.com/BioContainers/multi-package-containers/pull/1236) Last but not least, David wanted to get the Galaxy `diff` tool into the European Galaxy server. For that, a new PR was created against the tool repository from usegalaxy-eu. **Step 3 - request for installation**: [https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/318](https://github.com/usegalaxy-eu/usegalaxy-eu-tools/pull/318) Once this is merged, another bot installs all the new tools but also tool updates automatically every Saturday. As a result, the installed `diff` tool can be used on the European Galaxy server following this link: https://usegalaxy.eu/root?tool_id=diff That's it - 3 steps to get your tool exposed to thousands of researchers!
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