Installation¶
Stable release¶
Clone repo from github <https://github.com/lauren-mak/camp_binning>_.
- Set up the conda environment (contains, Snakemake) using
configs/conda/camp_binning.yaml. There are some compatibility issues that I haven’t ironed out (samtools and bowtie2 due to RedHat’s geriatric dependencies), so you may have to substitute in your own versions of those two tools.
- Set up the conda environment (contains, Snakemake) using
3. Make sure the installed pipeline works correctly. pytest only generates temporary outputs so no files should be created.
cd camp_binning
conda env create -f configs/conda/camp_binning.yaml
conda activate camp_binning
pytest .tests/unit/