Installation

Install from source

Clone the repository:

git clone https://github.com/mazzalab/STRmie-HD.git
cd STRmie-HD

Create the conda environment:

conda env create -f STRmie.yml

Activate the environment:

conda activate STRmie

Install the package:

pip install -e .

Install via Bioconda

If you already use Conda/Mamba, you can install STRmie-HD directly from the bioconda channel:

# (optional) ensure channels are configured
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --set channel_priority strict

# install
conda install -c bioconda strmie-hd
# or with mamba:
# mamba install -c bioconda strmie-hd

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Run via BioContainers (Docker)

A pre-built container image is available on Quay (BioContainers). Example:

docker pull quay.io/biocontainers/strmie-hd:1.0.0--pyhdfd78af_0

# show help
docker run --rm quay.io/biocontainers/strmie-hd:1.0.0--pyhdfd78af_0 strmie --help

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Verify installation

Help

strmie --help

Automated Testing with Pytest

The project includes a test suite that validates the core functionalities of both operational modes using example input and expected output files.
This ensures the tool works as intended after installation or modification.

Run tests with:

pytest tests/test_strmie.py

What it tests: Executes the full pipeline and compares the output Excel with the expected report.