recipe kalamari

A curated database of completed assemblies with taxonomy IDs

Homepage:

https://github.com/lskatz/kalamari

Documentation:

https://github.com/lskatz/Kalamari/blob/master/README.md

Developer docs:

https://github.com/lskatz/Kalamari

License:

CC / Creative Commons 4.0

Recipe:

/kalamari/meta.yaml

Kalamari is a curated database of assemblies and taxonomies. These assemblies are curated mainly for foodborne bacteria but have other taxa such as SARS-CoV-2 and Crytposporidium. Taxonomy has been modified from NCBI Taxonomy and has been minimalized to just what is needed here.

package kalamari

(downloads) docker_kalamari

versions:
5.7.1-0,  5.7.0-0,  5.6.3-0,  5.6.2-0,  5.6.1-0,  5.6.0-2,  5.6.0-0,  5.5.0-0,  5.4.1-1, 

5.7.1-0,  5.7.0-0,  5.6.3-0,  5.6.2-0,  5.6.1-0,  5.6.0-2,  5.6.0-0,  5.5.0-0,  5.4.1-1,  5.4.1-0,  5.4.0-0,  5.3.3-0,  5.3.2-0,  5.2.1-0

depends entrez-direct:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-module-build:

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 kalamari

and update with::

   mamba update kalamari

To create a new environment, run:

mamba create --name myenvname kalamari

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/kalamari:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/kalamari/README.html)