recipe gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Homepage:

https://github.com/Ecogenomics/GTDBTk

License:

GPL3 / GNU General Public v3 (GPLv3)

Recipe:

/gtdbtk/meta.yaml

Links:

doi: 10.1093/bioinformatics/btz848

package gtdbtk

versions:

2.4.0-1,  2.4.0-0,  2.3.2-0,  2.3.0-2,  2.3.0-1,  2.3.0-0,  2.2.6-1,  2.2.6-0,  2.2.5-0, 

2.4.0-1,  2.4.0-0,  2.3.2-0,  2.3.0-2,  2.3.0-1,  2.3.0-0,  2.2.6-1,  2.2.6-0,  2.2.5-0,  2.2.4-0,  2.2.3-1,  2.2.3-0,  2.2.2-0,  2.2.0-0,  2.1.1-1,  2.1.1-0,  2.1.0-5,  2.1.0-4,  2.1.0-3,  2.1.0-2,  2.1.0-1,  2.1.0-0,  2.0.0-2,  2.0.0-1,  2.0.0-0,  1.7.0-0,  1.6.0-0,  1.5.1-0,  1.5.0-0,  1.4.1-1,  1.4.1-0,  1.4.0-1,  1.4.0-0,  1.3.0-2,  1.3.0-1,  1.3.0-0,  1.2.0-1,  1.2.0-0,  1.1.1-0,  1.1.0-0,  1.0.2-3,  1.0.2-2,  1.0.2-1,  1.0.2-0,  1.0.1-1,  1.0.1-0,  1.0.0-0,  0.3.3-0,  0.3.2-2,  0.3.2-1,  0.3.2-0,  0.3.1-0,  0.3.0-1,  0.3.0-0,  0.2.2-0,  0.1.6-0,  0.1.5-0,  0.1.3-0

depends dendropy:

>=4.1.0

depends fastani:

1.32.*

depends fasttree:

>=2.1.9

depends hmmer:

3.*

depends mash:

>=2.0

depends numpy:

>=1.9.0

depends pplacer:

>=1.1.alpha17

depends prodigal:

>=2.6.2

depends pydantic:

>=1.9.2,<2

depends python:

>=3.6

depends skani:

>=0.2.0

depends tqdm:

>=4.35.0

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 gtdbtk

and update with::

   mamba update gtdbtk

To create a new environment, run:

mamba create --name myenvname gtdbtk

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/gtdbtk:<tag>

(see `gtdbtk/tags`_ for valid values for ``<tag>``)

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