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Installation

1. Clone the repository

git clone https://github.com/FDBoever/kmer-ord.git
cd kmer-ord

2. Create a fresh conda environment

Option A (recommended): use the provided environment.yml

conda env create -f environment.yml
conda activate kmerord-env

Option B: manual setup

conda create -n kmerord-env python=3.11 -c conda-forge
conda activate kmerord-env

conda install -c conda-forge numpy pandas scikit-learn umap-learn pacmap numba llvmlite biopython typer libspatialite python-igraph hnswlib hdbscan scipy leidenalg matplotlib seaborn setuptools==65.5.0

Tip: You can replace conda with mamba for faster installs.

3. Install the kmer-ord package

First ensure you are inside the kmer-ord directory (obtained from GitHub), and activated the conda environment

For users

pip install .

For developers (editable install)

pip install -e .

4. Set up external tools and databases

Finally, use kmer-ord to set up internal environments for external tools and downloading rRNA databases (this can take a while, so consider grabbing yourself a coffee) 

kmer-ord setup

5. Verify installation

Finally, check whether the tool is installed.

kmer-ord --help