Installation#
Recommended: Conda/Mamba (Bioconda)#
Install from Bioconda with conda:
conda install mirmachine -c bioconda -c conda-forge
Using mamba is faster for dependency solving:
conda install mamba -c conda-forge
mamba install mirmachine -c bioconda -c conda-forge
From Source (Local Development)#
From the repository root:
conda env create -f environment.yml
conda activate mirmachine
pip install -e .
MirMachine now ships a pyproject.toml build definition, so pip installs use
the standard PEP 517 build backend by default.
The environment file includes Python dependencies plus required command-line
tools used by the workflow (for example snakemake, infernal,
samtools, bedtools, gawk, and moreutils).
Verify Installation#
Check CLI availability:
MirMachine.py --help