There are several types of workspaces to consider when thinking about cloning a workspace to start your project.ĭata-Oriented Workspaces - These workspaces hold data for AnVIL open or controlled-access data sets or cohorts exported from Gen3. You may start with a blank workspace, but typically you will start by cloning a workspace containing the data or analysis you require. In general, to perform an analysis in a workspace, you set up the data and workflows you require and then launch a cloud environment to execute the analysis over the data and write out results to the workspace storage bucket. Terra workspaces can also run Docker containerized workflows written in WDL. Terra workspaces support interactive analysis with Jupyter notebooks, Bioconductor and Galaxy. Workspaces can also save the output generated by running an analysis with a workspace’s associated “cloud environment.” Terra workspaces typically hold genomic data and subject-level phenotypic and sample processing data and are configured with analysis tools such as notebooks and Docker images. In Terra, you use workspaces to configure and run analyses and share results. To allow your dbGaP data request approvals to flow through to Terra and Gen3, you will need to link your eRA commons ID with both platforms.įor instructions on requesting data access see Requesting Data Access and Discovering Data. To send artificial cohorts from Gen3 to Terra for Analysis, you will need to link your Gen3 and Terra accounts. Likewise, with a Google account, you can register with Gen3 and browse publicly accessible datasets or register with Dockstore and browse tools and workflows.
An overview of cloud compute costs and setting up billing.Īll you need is a Google account to register with Terra and browse AnVIL’s publicly accessible workspaces.The following is a guided walk-through of the AnVIL / Terra documentation with a focus on onboarding and preparing new users to run genomic analyses in the cloud. For example see the guides for data analysts, investigators, developers, instructors, and data contributors. To complement this onboarding and introductory section, the AnVIL team is in the process of developing persona-specific guides and tutorials.
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About AnVIL’s DocumentationĪnVIL’s training materials curate, and augment existing component and tool documentation, and show how to use AnVIL’s parts together to accomplish the goals of AnVIL’s different user personas. In addition to Docker-based analysis workflows, AnVIL supports popular interactive analysis tools such as Jupyter notebooks, Bioconductor, RStudio, and Galaxy.īy operating in the cloud, AnVIL users can scale analyses from a single computer to thousands and securely share data, workflows, and reproducible results with collaborators and colleagues.
AnVIL enables researchers to analyze high-value open and controlled access genomic datasets with popular analysis tools in a secure cloud computing environment.ĪnVIL uses Terra as its analysis platform, Gen3 for data search and artificial cohort creation, and Dockstore as a repository for Docker-based genomic analysis tools and workflows. The AnVIL platform is an NHGRI supported data commons running on the Google Cloud Platform (GCP).
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