recipe checkm-genome

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Homepage:

https://github.com/Ecogenomics/CheckM

Documentation:

https://ecogenomics.github.io/CheckM

License:

GPL3 / GPL-3.0-or-later

Recipe:

/checkm-genome/meta.yaml

package checkm-genome

versions:

1.2.3-1,  1.2.3-0,  1.2.2-1,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.11-0,  1.1.10-0,  1.1.9-0, 

1.2.3-1,  1.2.3-0,  1.2.2-1,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.11-0,  1.1.10-0,  1.1.9-0,  1.1.8-0,  1.1.3-1,  1.1.3-0,  1.1.2-2,  1.1.2-1,  1.1.2-0,  1.1.1-0,  1.1.0-1,  1.1.0-0,  1.0.18-0,  1.0.17-0,  1.0.16-0,  1.0.13-1,  1.0.13-0,  1.0.12-0,  1.0.11-1,  1.0.11-0,  1.0.7-0,  1.0.5-0

depends dendropy:

>=4.5.2

depends hmmer:

>=3.1b1

depends matplotlib-base:

>=3.5.1

depends numpy:

>=1.21.3

depends pplacer:

1.1.alpha19

depends prodigal:

>=2.6.1

depends pysam:

>=0.19.0

depends python:

>=3.6,<3.12

depends scipy:

>=1.7.3

depends wget:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install checkm-genome

and update with::

   mamba update checkm-genome

To create a new environment, run:

mamba create --name myenvname checkm-genome

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/checkm-genome:<tag>

(see `checkm-genome/tags`_ for valid values for ``<tag>``)

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