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--- # The Galaxy Tool Shed .footnote[Tip: press `P` to view the presenter notes] ??? Presenter notes contain extra information which might be useful if you intend to use these slides for teaching. Press `P` again to switch presenter notes off --- Tool Shed is to Galaxy as App Store is to iPhone. It is a free service that hosts repositories containing Galaxy Tools. Installing from the Tool Shed takes care of - dependencies - reference data tables - configuration files --- Main Tool Shed (MTS) runs at http://toolshed.g2.bx.psu.edu and serves all Galaxies worldwide. Everybody can create a repository. Every repository is public including the whole history. Local sheds can be run e.g. for private or custom-licensed tools. ??? We discourage running local TS. --- ## Vocabulary * `wrapper` or `tool definition file` - The XML file that describes to Galaxy how the underlying software works, allowing Galaxy to render UI and execute the software in the right way. -- * `repository` - A versioned code archive with tool(s) in Tool Shed. -- * `revision` and `installable revision` - Every TS repo update generates a new revision but only certain (reproducibility-affecting) changes generate a new revision installable to Galaxy as a new version. ??? Every TS repo update can be propagated to the Galaxy though. --- ## Overview * Tool Shed is a host (not a development) platform. -- * Tool Development repository should be linked from the TS repository. -- * Tool Shed allows administrators to pick any installable revision. -- * Multiple installable revisions of any repository can be present in Galaxy. --- ![TS_big_picture.png](../../images/TS_big_picture.png) --- class: normal ## Galaxy's Configuration List of available sheds is defined in `tool_sheds_conf.xml` and Galaxy comes with the MTS enabled and the TTS disabled. ```xml <?xml version="1.0"?> <tool_sheds> <tool_shed name="Galaxy Main Tool Shed" url="https://toolshed.g2.bx.psu.edu/"/> <!-- Test Tool Shed should be used only for testing purposes. <tool_shed name="Galaxy Test Tool Shed" url="https://testtoolshed.g2.bx.psu.edu/"/> --> </tool_sheds> ``` --- class: normal ## Simple TS repository (remove_beginning) ```shell . ├── .shed.yml ├── remove_beginning.pl ├── remove_beginning.xml └── test-data ├── 1.bed └── eq-removebeginning.dat ``` --- class: normal ## Simple TS repository (remove_beginning) ```shell . ├── .shed.yml # metadata file ├── remove_beginning.pl # script that performs the requested ├── remove_beginning.xml # tool wrapper └── test-data # this one is descriptive ├── 1.bed # test input file └── eq-removebeginning.dat # test output file ``` --- class: normal ### .shed.yml file Contains tool's metadata. ```yml categories: - Text Manipulation description: Remove lines from the beginning of a file. long_description: | This tool removes the specified number of lines from the beginning of the input dataset. name: remove_beginning owner: devteam remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning type: unrestricted ``` --- class: normal ## Complex TS Repository ```shell . ├── .shed.yml ├── macros.xml ├── seqtk_comp.xml ├── seqtk_sample.xml ├── seqtk_seq.xml ├── seqtk_trimfq.xml ├── test-data │ ├── seqtk_trimfq.fq ... │ ├── seqtk_trimfq_be.fq │ └── seqtk_trimfq_default.fq └── tool_dependencies.xml ``` --- class: normal ## Complex TS Repository ```shell . ├── .shed.yml ├── macros.xml # defines xml macros usable in other xml files ├── seqtk_comp.xml # wrapper for a tool ├── seqtk_sample.xml # wrapper for tool #2 ├── seqtk_seq.xml # wrapper for tool #3 ├── seqtk_trimfq.xml # wrapper for tool #4 ├── test-data │ ├── seqtk_trimfq.fq # bunch of test data ... │ ├── seqtk_trimfq_be.fq │ └── seqtk_trimfq_default.fq └── tool_dependencies.xml # file that describes Galaxy how to get TS-supplied dependencies to fulfill the <requirements> in tool wrappers ``` --- ### seqtk requirements Requirements of the wrapper. ```xml <requirements> <requirement type="package" version="1.2">seqtk</requirement> </requirements> ``` Galaxy is aiming to be dependency resolution agnostic. --- # Approach * We aim to make Galaxy resolver-independent but Conda-oriented. * What resolver is going to be used for the tool dependency is determined at runtime and prioritised in the config file `dependency_resolvers_conf.xml`. ```xml <dependency_resolvers> <tool_shed_packages /> <galaxy_packages /> <conda /> <galaxy_packages versionless="true" /> <conda versionless="true" /> <!-- other resolvers <tool_shed_tap /> <homebrew /> --> </dependency_resolvers> ``` --- class: smaller ### seqtk Conda package ```yml package: name: seqtk version: 1.2 source: fn: v1.2.tar.gz url: https://github.com/lh3/seqtk/archive/v1.2.tar.gz md5: 255ffe05bf2f073dc57abcff97f11a37 build: number: 0 requirements: build: - gcc # [not osx] - llvm # [osx] - zlib run: - zlib about: home: https://github.com/lh3/seqtk license: MIT License summary: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format test: commands: - seqtk seq ``` --- ## Thank you! This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors!
Marius van den Beek
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