📋 Requirements

R 4.2.0

🛠️ Installation

git clone [email protected]:clbenoit/GermlineVarDB.git

⚙️ Configuration

Edit the config file

• cache_directory : directory to store GermlineVarDB cache files in. Necessary for good app performances. If NULL, a temporary directory will be used and cache will be lost on computer restart
• multiqc : Path where multiqc run reports are stored. Will be soon compatible with Apache server URL
• db_path : Path where you genomic variation database is stored
• prefix : Name of you Genomic variation stuctured database
• use_browser : Do you want to activate genome browser functionnality to visualize bam files ? (TRUE|FALSE)
• [Optional] browser_server_path : In the case of a local JBrowseR installation, not intended for production use
• [Optional] browser_client_url: Url to your JBrowseR server, files should be accessible from the WebBrowser used to access the Shiny app

For example prefix = "lung_variations" db_path = "/home/my_databases/" Will set up GermlineVarDB to use the following SQLite database : /home/my_databases/lung_variations.db

🚀 Run the application

Go to the app root directory and run

Sys.setenv(MY_VARIABLE = "default"); shiny::runApp()

Demo app

💻 Run demo locally

Go to the app root directory and run

Sys.setenv(MY_VARIABLE = "demo"); shiny::runApp() Skip references download and disable genome browser on demo app

Sys.setenv(MY_VARIABLE = "demo_browser"); shiny::runApp() Will download genome reference file on first call before to start the app

🌐 Live demo App

See live demo

🧬 Manage your genomic variations database

See https://github.com/clbenoit/GermlineVarDBTools

🔜 Incoming features

• Possibility for the user to save filters and parameters presets and choose a default one
• Add in silico panel lists usable as filtering option
• Possibility for the user to upload a list of preferential transcripts, default use the canonical one in sample variants table -> cleaner view

⚠️ Troubleshouting