q2-checkm

QIIME 2 plugin for assessing the quality of (meta)genomes using CheckM.

Installation

Conda environment

You can install q2-checkm in an existing QIIME 2 environment or create a new environment by following the instructions for the tiny distribution.

Install pplacer

pplacer is only available through conda for Linux - you can use our script to fetch the binary directly:

curl -s https://raw.githubusercontent.com/bokulich-lab/q2-checkm/main/install-pplacer.sh | bash

Install remaining dependencies

mamba install -c bioconda -c conda-forge -c qiime2 -c defaults \
  dendropy "altair<5.0.0" hmmer prodigal pysam matplotlib numpy q2templates

Install checkm and q2-checkm

pip install checkm-genome git+https://github.com/bokulich-lab/q2-checkm.git

Refresh QIIME 2 cache

qiime dev refresh-cache

Notes on CheckM version

CheckM version currently used by q2-checkm is pinned to a specific commit: https://github.com/Ecogenomics/CheckM.git@8b42a8ca13dda3a967e2247efe6032f9df1bd434. We are not using the corresponding version available through conda, as it has pplacer as a pinned dependency (and this dependency cannot be resolved on some systems). Instead, we are manually taking care of checkm's dependencies and just installing it through pip.

Notes on Altair version

Installing q2-checkm in an existing QIIME 2 environment by following the instructions above may case Altair to be downgraded to version <5. Proceed with caution!