recipe chewbbaca

A complete suite for gene-by-gene schema creation and strain identification.

Homepage:

https://github.com/B-UMMI/chewBBACA

Documentation:

https://chewbbaca.readthedocs.io/en/latest/index.html

License:

GPL3 / GPL-3.0-or-later

Recipe:

/chewbbaca/meta.yaml

Links:

doi: 10.1099/mgen.0.000166

chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.

package chewbbaca

versions:

3.3.10-0,  3.3.9-0,  3.3.8-0,  3.3.7-0,  3.3.6-0,  3.3.5-0,  3.3.4-0,  3.3.3-0,  3.3.2-0, 

3.3.10-0,  3.3.9-0,  3.3.8-0,  3.3.7-0,  3.3.6-0,  3.3.5-0,  3.3.4-0,  3.3.3-0,  3.3.2-0,  3.3.1-0,  3.3.0-1,  3.3.0-0,  3.2.0-0,  3.1.2-0,  3.1.1-0,  3.1.0-0,  3.0.0-0,  2.8.5-1,  2.8.5-0,  2.8.4-0,  2.7.0-0,  2.6.0-0,  2.5.6-0,  2.5.5-0,  2.5.4-0,  2.5.2-0,  2.5.1-0,  2.1.0-0,  2.0.17.2-0,  2.0.17.1-0,  2.0.16-0,  2.0.15-0,  2.0.12-2,  2.0.8-2,  2.0.8-0,  2.0.6-0,  1.0-0

depends biopython:

>=1.79

depends blast:

>=2.9.0

depends fasttree:

>=2.1.11

depends mafft:

>=7.505

depends numpy:

>=1.24.3

depends pandas:

>=1.5.1,<2.1

depends plotly:

>=5.8.0

depends pyrodigal:

>=3.0.0

depends python:

>=3.7

depends requests:

>=2.27.1

depends scipy:

>=1.10.1

depends sparqlwrapper:

>=2.0.0

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 chewbbaca

and update with::

   mamba update chewbbaca

To create a new environment, run:

mamba create --name myenvname chewbbaca

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/chewbbaca:<tag>

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

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