# Galaxy Ecosystem and Projects *The architecture of the ecosystem.* --- ### Learning Questions - What projects make up the Galaxy ecosystem? - How do different Galaxy projects interact? - What tools are available for developers vs administrators? --- ### Learning Objectives - Identify the major projects in the Galaxy ecosystem - Understand the difference between user-facing and developer tools - Learn about Galaxy communication channels --- ### Please Interrupt! We're here to answer your questions about Galaxy architecture! --- class: enlarge200 **Chat:** [galaxyproject Lobby](https://matrix.to/#/#galaxyproject_Lobby:gitter.im) (via Element) **GitHub:** [github.com/galaxyproject ](https://github.com/galaxyproject) **Bluesky:** [bsky.app/profile/galaxyproject.bsky.social](https://bsky.app/profile/galaxyproject.bsky.social) **Mastodon:** [@galaxyproject](https://mstdn.science/@galaxyproject) **LinkedIn:** [Galaxy Project](https://www.linkedin.com/groups/4907635/) --- ### The **/galaxyproject** projects *The architecture of the ecosystem.* ??? Too many to cover all but we'll cover some of the big ones in a few big categories. User-facing applications, projects for Galaxy plugin developers, and projects for Galaxy administrators. --- ### Matrix Community with Element  Access via Element client or any Matrix client at https://matrix.to/#/#galaxyproject_Lobby:gitter.im --- class: reduce70 center More links we'll mention as we go through the slides: - https://matrix.to/#/#galaxyproject_Lobby:gitter.im - https://matrix.to/#/#galaxyproject_dev:gitter.im - https://matrix.to/#/#galaxyproject_admins:gitter.im - https://matrix.to/#/#galaxyproject_FederatedGalaxy:gitter.im - https://matrix.to/#/#galaxyproject_bioblend:gitter.im - https://matrix.to/#/#galaxyproject_ephemeris:gitter.im - https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im - https://matrix.to/#/#galaxy-iuc_iuc:gitter.im - https://matrix.to/#/#bgruening_docker-galaxy-stable:gitter.im - https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im - https://matrix.to/#/#biocontainers_Lobby:gitter.im - https://matrix.to/#/#bioconda_Lobby:gitter.im Working group chats linked at https://galaxyproject.org/community/wg/. --- class: enlarge200 **User-Facing Applications** --- class: enlarge150 [galaxyproject/**galaxy** ](https://github.com/galaxyproject/galaxy) The main Galaxy application. Web interface, database model, job running, etc... Also includes other web applications including the **ToolShed**. --- class: enlarge150 [galaxyproject/**training-material** ](https://github.com/galaxyproject/training-material)  Galaxy training material for scientists, developers, and admins. Powers *https://training.galaxyproject.org/*. --- class: enlarge150 [galaxyproject/**hub** ](https://github.com/galaxyproject/galaxy-hub) The Galaxy Hub is the community and documentation hub for the Galaxy Project. It is maintained by the community through this GitHub repository. It is a static website built using the metalsmith static site generator. Powers *https://galaxyproject.org/*. --- class: enlarge150 [**usegalaxy-eu/galaxy-social** ](https://github.com/usegalaxy-eu/galaxy-social) Content distribution system for publishing to multiple social media platforms. Post once, share across Mastodon, Bluesky, Matrix, Slack, and LinkedIn with automatic formatting. --- class: enlarge150 [galaxyproject/**galaxy_codex** ](https://github.com/galaxyproject/galaxy_codex) Community resource repository for Galaxy users and contributors. Provides access to the Galaxy Community Catalog featuring tools, training materials, and workflows. Galaxy Labs for creating customized community subdomain pages. --- class: enlarge150 [galaxyproject/**bioblend** ](https://github.com/galaxyproject/bioblend) Official Python client for the Galaxy, ToolShed, and CloudMan APIs. Best documented path to scripting the Galaxy API. --- A standalone client library for the Galaxy API, built using the type definitions from the main Galaxy client. https://www.npmjs.com/package/@galaxyproject/galaxy-api-client --- - [galaxyproject/**blend4php**](https://github.com/galaxyproject/blend4php) - [galaxyproject/**blend4j**](https://github.com/galaxyproject/blend4j) - [**chapmanb/clj-blend**](https://github.com/chapmanb/clj-blend) Galaxy API bindings for other languages, less actively maintained. --- class: enlarge150 [**bgruening/docker-galaxy-stable** ](https://github.com/bgruening/docker-galaxy-stable) High quality Docker containers for stable Galaxy environments. Releases corresponding to each new version of Galaxy. Many flavors available. --- class: white  --- class: enlarge200 **For Plugin Developers** --- class: reduce70 center [galaxyproject/**tools-iuc** ](https://github.com/galaxyproject/tools-iuc) Galaxy tools maintained by the *IUC* ("Intergalactic Utilities Commission"). A variety of tools, generally of high quality including many of the core tools for Galaxy main. Demonstrates *current tool development best practices* - development on github and then deployed to test/main ToolSheds [galaxyproject/**tools-devteam** ](https://github.com/galaxyproject/tools-devteam) Many older tools appearing on usegalaxy.org. --- class: center reduce70 ### Tools Aside - More Repositories Other repositories with high quality tools: * [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) * [ENCODE tools](https://github.com/modENCODE-DCC/Galaxy) * [Biopython repo](https://github.com/biopython/galaxy_packages) * [Galaxy Proteomics repo](https://github.com/galaxyproteomics/tools-galaxyp) * [Greg von Kuster's repo](https://github.com/gregvonkuster/galaxy-csg) * [TGAC repo](https://github.com/TGAC/tgac-galaxytools) * [AAFC-MBB Canada repo](https://github.com/AAFC-MBB/Galaxy/tree/master/wrappers) * [Mark Einon's repo](https://gitlab.com/einonm/galaxy-tools) --- [galaxyproject/**iwc** ](https://github.com/galaxyproject/iwc) Intergalactic Workflow Commission. Hosting workflows and defining best practices for publishing workflows. https://matrix.to/#/#galaxyproject_iwc:gitter.im --- class: enlarge150 [galaxyproject/**planemo** ](https://github.com/galaxyproject/planemo) Command-line utilities to assist in the development of Galaxy tools and workflows. Linting, testing, deploying to ToolSheds... *The best practice approach for Galaxy tool development!* [galaxyproject/**planemo-machine** ](https://github.com/galaxyproject/planemo-machine) Builds Galaxy environments for Galaxy tool development including Docker container, virtual machines, Google compute images --- [galaxyproject/**galaxy-language-server** ](https://github.com/galaxyproject/galaxy-language-server)  Language server implementation for Galaxy tools. Visual Studio Code extension for tool development. Test execution, code completion, best practices, documentation tooltips, etc.. --- class: enlarge150 [galaxyproject/**starforge** ](https://github.com/galaxyproject/starforge)  Build Galaxy framework dependencies as Python wheels when needed. --- class: enlarge150 [galaxyproject/**cargo-port** ](https://github.com/galaxyproject/cargo-port)  Provides stable URLs and caching for application links, etc.. An important layer for reproducibility but largely transparent. --- class: enlarge200 **For Deployers and Admins** --- class: enlarge150 galaxyproject/**{ansible-\*, \*-playbook}**<br> usegalaxy-eu/**{ansible-\*, \*-playbook}** [Ansible](https://www.ansible.com/) components to automate almost every aspect of Galaxy installation and maintenance. Ansible is an advanced configuration management system These playbooks are used to maintain Galaxy main, cloud and Docker images, virtual machines, ... --- class: enlarge150 [galaxyproject/**gravity** ](https://github.com/galaxyproject/gravity) A process manager (supervisor) and management tools for Galaxy servers. `galaxyctl` which is used to manage the starting, stopping, and logging of Galaxy's various processes. `galaxy` which can be used to run a Galaxy server in the foreground. --- class: enlarge150 [galaxyproject/**galaxy-helm** ](https://github.com/galaxyproject/galaxy-helm) Kubernetes helm chart for deploying Galaxy. Leveraged by cloudlaunch and CloudMan but usable standalone. --- class: enlarge150 [galaxyproject/**pulsar** ](https://github.com/galaxyproject/pulsar)  Distributed job execution engine for Galaxy. Stages data, scripts, configuration. Can run jobs on Windows machines. Can act as its own queuing system or access an existing cluster DRM. --- class: enlarge150 [galaxyproject/**ephemeris** ](https://github.com/galaxyproject/ephemeris) Library and CLI for managing Galaxy plugins - tools, index data, and workflows. Layer on top of BioBlend building useful utilities for working with the Galaxy API from an administrator perspective. --- class: enlarge150 [galaxyproject/**gxadmin** ](https://github.com/galaxyproject/gxadmin) Handy command-line utility for Galaxy administrators. --- class: enlarge150 ### ephemeris vs gxadmin Ephemeris generally talks to the Galaxy API and is a pure Python project, gxadmin talks directly to the Galaxy database and relevant files. --- ### Total Perspective Vortex [galaxyproject/total-perspective-vortex **](https://github.com/galaxyproject/total-perspective-vortex)  TotalPerspectiveVortex (TPV) provides an installable set of dynamic rules for the Galaxy application that can route entities (Tools, Users, Roles) to appropriate job destinations based on a configurable yaml file. --- class: enlarge150 [**usegalaxy-eu/tiaas2 **](https://github.com/usegalaxy-eu/tiaas2)  Django-based infrastructure for creating pools of users, etc.. for training events and connecting them to Galaxy. --- ### Some (out of many) friends of the project   Check out dev training materials "Tool Dependencies and Conda" and "Tool Dependencies and Containers" for more context. --- ### Putting it all together  ??? TODO: cover gxformat2 --- class: enlarge200 [galaxyproject/**galaxy** ](https://github.com/galaxyproject/galaxy) The rest of the slides will focus on the core repository.
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