recipe el_gato

Perform Legionella pneumophila Sequence Based Typing (SBT) from short reads or assemblies.

Homepage:

https://github.com/appliedbinf/el_gato

Documentation:

https://github.com/appliedbinf/el_gato/blob/1.20.2/README.md

License:

MIT / MIT

Recipe:

/el_gato/meta.yaml

package el_gato

versions:

1.20.2-0,  1.20.1-0,  1.19.0-0,  1.18.2-0,  1.18.1-0,  1.18.0-0,  1.15.2-0,  1.15.0-0,  1.14.4-0

depends blast:

>=2.13

depends colorama:

depends fpdf2:

depends ispcr:

>=33.0

depends minimap2:

>=2.24

depends nextflow:

depends packaging:

depends python:

>=3.8,<3.12

depends samtools:

>=1.15.1

requirements:

additional platforms:

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 el_gato

and update with::

   mamba update el_gato

To create a new environment, run:

mamba create --name myenvname el_gato

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/el_gato:<tag>

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

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