https://github.com/artdotlis/linkatlas

A collection of libraries for gathering possible links between strains and taxonomy from different sources like literature and sequence databases.
https://github.com/artdotlis/linkatlas

identifier microbial-identifier python

Last synced: 8 months ago
JSON representation

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

• Host: GitHub
• URL: https://github.com/artdotlis/linkatlas
• Owner: artdotlis
• License: mit
• Created: 2025-09-26T14:57:09.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2025-10-24T12:11:29.000Z (8 months ago)
• Last Synced: 2025-10-24T14:12:28.794Z (8 months ago)
• Topics: identifier, microbial-identifier, python
• Language: Python
• Homepage:
• Size: 162 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# LinkAtlas - links between strains and taxonomy

[![release: 0.1.0](https://img.shields.io/badge/rel-0.1.0-blue.svg?style=flat-square)](https://gitlab.int.dsmz.de/artur.lissin/linkatlas#)

[![MIT LICENSE](https://img.shields.io/badge/License-MIT-brightgreen.svg?style=flat-square)](https://choosealicense.com/licenses/mit/)

[![Documentation Status](https://img.shields.io/badge/docs-GitHub-blue.svg?style=flat-square)](https://artdotlis.github.io/linkatlas/)

[![main](https://github.com/artdotlis/linkatlas/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/artdotlis/linkatlas/actions/workflows/main.yml)

---

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:

   ```sh

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

   cd cafi

   ```

#### Docker

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

   ```sh

   devcontainer up --workspace-folder .

   devcontainer exec --workspace-folder . bash

   ```

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

   ```sh

   make dev

   make runAct

   ```

## Contributors

- Isabel Schober