Australian BioCommons, University of Melbourne, Melbourne, VIC 3052, Australia.
Channing Division of Network Medicine, Harvard Medical School, Boston, MA 02115, United States.
Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae486.
The Galaxy application is a popular open-source framework for data intensive sciences, counting thousands of monthly users across more than 100 public servers. To support a growing number of users and a greater variety of use cases, the complexity of a production-grade Galaxy installation has also grown, requiring more administration effort. There is a need for a rapid and reproducible Galaxy deployment method that can be maintained at high-availability with minimal maintenance.
We describe the Galaxy Helm chart that codifies all elements of a production-grade Galaxy installation into a single package. Deployable on Kubernetes clusters, the chart encapsulates supporting software services and implements the best-practices model for running Galaxy. It is also the most rapid method available for deploying a scalable, production-grade Galaxy instance on one's own infrastructure. The chart is highly configurable, allowing systems administrators to swap dependent services if desired. Notable uses of the chart include on-demand, fully-automated deployments on AnVIL, providing training infrastructure for the Bioconductor project, and as the AWS-recommended solution for running Galaxy on the Amazon cloud.
The source code for Galaxy Helm is available at https://github.com/galaxyproject/galaxy-helm, the corresponding Helm package at https://github.com/CloudVE/helm-charts, and the required Galaxy container image https://github.com/galaxyproject/galaxy-docker-k8s.
Galaxy 应用程序是一个流行的开源框架，适用于数据密集型科学，在 100 多个公共服务器上拥有数千名月度用户。为了支持越来越多的用户和更多样化的用例，生产级 Galaxy 安装的复杂性也在增加，需要更多的管理工作。需要有一种快速且可重复的 Galaxy 部署方法，可以以最小的维护成本保持高可用性。
我们描述了 Galaxy Helm 图表，它将生产级 Galaxy 安装的所有元素编码到一个单独的包中。可在 Kubernetes 群集上部署，该图表封装了支持软件服务，并实现了运行 Galaxy 的最佳实践模型。它也是在自己的基础架构上快速部署可扩展生产级 Galaxy 实例的最有效方法。该图表具有高度可配置性，允许系统管理员根据需要交换依赖服务。该图表的一些重要用途包括在 AnVIL 上按需、全自动部署，为 Bioconductor 项目提供培训基础设施，以及作为在亚马逊云中运行 Galaxy 的 AWS 推荐解决方案。
Galaxy Helm 的源代码可在 https://github.com/galaxyproject/galaxy-helm 获得，相应的 Helm 包可在 https://github.com/CloudVE/helm-charts 获得，所需的 Galaxy 容器映像可在 https://github.com/galaxyproject/galaxy-docker-k8s 获得。
