Installing CheckM (WSL)
CheckM is a tool for assessing the quality of metagenome-assembled genomes (MAGs).
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Create a conda environment and install dependencies
conda create -n checkm python=3.9
conda activate checkm
conda install -c bioconda numpy matplotlib pysam
conda install -c bioconda hmmer prodigal pplacer
pip3 install checkm-genome
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Download reference data
Download the reference dataset from Zenodo:
Set the environment variable to point to the reference data:
export CHECKM_DATA_PATH=/path/to/my_checkm_data
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Installing CheckM (Mac)
Install dependencies using Homebrew
brew install hmmer
brew install prodigal
brew install pplacer
Install Python packages
pip3 install numpy
pip3 install matplotlib
pip3 install pysam
pip3 install checkm-genome
Download reference data
Download the reference dataset from Zenodo:
Set the environment variable to point to the reference data:
export CHECKM_DATA_PATH=/path/to/my_checkm_data