Pulling feat/jbrowse into develop#1212
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…sions The vite and vitest dependencies are upgraded to their latest major versions to take advantage of new features, performance improvements, and bug fixes.
This commit introduces the jbrowse application with necessary configuration files, including vite config, tsconfig, and environment variables. It sets up the basic layout with header, navbar, and footer components, along with routing and theming. The application uses Logto for authentication and Apollo Client for GraphQL data fetching.
The jbrowse react app2 dependency was added to the dictybase-jbrowse package. This allows the dictybase-jbrowse app to use the jbrowse react app2 library.
The change migrates the jbrowse app from @vitejs/plugin-react to @vitejs/plugin-react-swc. This migration improves the build performance and reduces the build time.
Added vite environment variables to allow for type checking of environment variables used in the application.
…pment This commit introduces the initial JBrowse configuration file for the development environment. It defines the assembly and a feature track, setting up the basic structure for JBrowse functionality.
The new script allows serving local data files for development and testing purposes, which is essential for running JBrowse 2 with custom data sources.
…isualization The JBrowseApp is now integrated into the application, utilizing a configuration file and a test plugin to enable genome visualization. The createViewState hook initializes the JBrowse view state with the specified configuration and plugins.
This commit introduces a new plugin called "GeneInfoPlugin" that fetches and displays gene information in a panel within the JBrowse genome browser. It fetches data from a GraphQL endpoint and renders the gene ID, name, and description.
The JBrowseApp was integrated, and the view state was configured using createViewState. The TestPlugin was added, and the access control was set to public.
This commit removes code that is required for a minimal jbrowse instance to run.
…compatibility The application now uses ReactDOM.createRoot instead of ReactDOM.render to be compatible with React 18.
An ESLint configuration has been added to improve code quality and consistency.
This commit documents known issues encountered during the development of the JBrowse application, along with their corresponding solutions. This information will help developers troubleshoot common problems and ensure a smoother development experience.
…elopment The README file is updated with a quickstart guide that provides instructions on how to run the application for local development with minimal configuration. It includes steps for installing dependencies, preparing FASTA files, generating a config.json file, and preparing GFF3 files.
…e.json The `faidx` and `add-assembly` scripts were added to the package.json file to provide convenient commands for generating FASTA index files and adding assembly configurations to JBrowse 2. The static-server command was updated to serve the public directory.
The README has been updated to include detailed instructions for setting up JBrowse, including generating the Fasta index file, serving static files, generating the config.json file, and running the application. The instructions now use yarn workspaces to execute commands within the @dictybase/jbrowse package.
The documentation has been updated to include a detailed workflow for updating the JBrowse configuration, including steps for generating index files, uploading to storage, modifying the local configuration, and deploying changes. This provides a clear guide for developers on how to properly update the JBrowse instance.
This commit introduces a new feature panel in the JBrowse plugin that displays gene information fetched from a GraphQL API. The panel is displayed when a gene feature is selected. The code was formatted to improve readability.
The application now loads configuration from config.json instead of config.dev.json. The import of ACCESS from "@dictybase/auth" was removed, as it was not being used.
…e dependencies The fontsource-roboto import was removed to reduce the number of dependencies and streamline the project's setup.
The initial JBrowse configuration file is added. This configuration sets up the assembly with the reference sequence track, which uses the IndexedFastaAdapter to fetch sequence data from a local server.
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