recipe centreseq

Fast generation of core genome from bacterial strains

Homepage:

https://github.com/bfssi-forest-dussault/centreseq

Developer docs:

https://github.com/BFSSI-Bioinformatics-Lab/centreseq

License:

MIT / MIT

Recipe:

/centreseq/meta.yaml

package centreseq

versions:

0.3.8-0,  0.3.0-0,  v0.2.3-0

depends biopython:

>=1.74

depends click:

>=7.0

depends mmseqs2:

9-d36de

depends muscle:

depends pandas:

>=0.24.0

depends prokka:

depends pytest:

>=5.0.1

depends python:

>=3.7

depends scipy:

>=1.1

depends seaborn:

>=0.9.0

depends tqdm:

>=4.39.0

depends xlsxwriter:

>=1.1.8

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 centreseq

and update with::

   mamba update centreseq

To create a new environment, run:

mamba create --name myenvname centreseq

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/centreseq:<tag>

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

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