LinkAtlas - links between strains and taxonomy

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A collection of libraries for gathering possible links between strains and taxonomy from different sources like literature and sequence databases.

Installation - Development

Prerequisites

• GNU/Linux
• Docker (optional)
• Docker Compose (optional)
• Dev Container CLI (optional)

Steps

1. Clone the repository:

   git clone https://github.com/LeibnizDSMZ/cafi.git
   cd cafi

Docker

2. If using Docker, start the development container manually or use VSCode:

   devcontainer up --workspace-folder .
   devcontainer exec --workspace-folder . bash

3. Create and activate a virtual environment (inside docker the container):

   make dev
   make runAct

Contributors

• Isabel Schober