Strain Authentication and Identification Methods - saim#

saim (Strain Authentication and Identification Methods) is a Python toolkit for reproducible identification, authentication, and metadata handling of microbial strains. It provides utilities for validating strain metadata, harmonizing identifiers, running identification workflows, and exporting results for downstream analysis.

Installation - Development#

Prerequisites#

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

Steps#

Clone the repository:

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

Docker#

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

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

Create and activate a virtual environment (inside docker the container):
```
make dev
make runAct
```

Local#

Create and activate a virtual environment:

python -m venv .venv
source .venv/bin/activate

Install the dependencies:

pip install .
pip install -r configs/dev/requirements.dev.txt
pip install -r configs/dev/requirements.test.txt
pip install -r configs/dev/requirements.docs.txt

Contributors#

Artur Lissin
Julius Witte