recipe mgkit

Metagenomics Framework

Homepage:

https://github.com/frubino/mgkit

License:

GPL2 / GPL-2.0-or-later

Recipe:

/mgkit/meta.yaml

Links:

biotools: mgkit, doi: 10.6084/m9.figshare.1588384

package mgkit

(downloads) docker_mgkit

versions:
0.5.8-4,  0.5.8-3,  0.5.8-2,  0.5.8-1,  0.5.8-0,  0.5.6-1,  0.5.6-0,  0.5.5-0,  0.5.4-0, 

0.5.8-4,  0.5.8-3,  0.5.8-2,  0.5.8-1,  0.5.8-0,  0.5.6-1,  0.5.6-0,  0.5.5-0,  0.5.4-0,  0.5.3-0,  0.5.2-0,  0.5.1-0,  0.5.0-0,  0.4.3-1,  0.4.3-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.4-0,  0.3.3-0,  0.3.0-0,  0.2.2-0

depends click:

>=6

depends future:

depends htseq:

>=0.9.1

depends libgcc:

>=13

depends matplotlib-base:

>=2

depends msgpack-python:

>=0.5.6

depends networkx:

depends numpy:

>=1.9.2

depends pandas:

>=1.1.3

depends pyarrow:

>=2.0.0

depends pymongo:

>=3.1.1

depends pysam:

>=0.14

depends pytables:

>=3.4.2

depends python:

>=3.9,<3.10.0a0

depends python_abi:

3.9.* *_cp39

depends pyvcf:

>=0.6.0

depends requests:

depends scipy:

>=0.15.1

depends semidbm:

>=0.5.1

depends statsmodels:

>=0.12

depends tqdm:

>=4.0

requirements:

additional platforms:
linux-aarch64

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 mgkit

and update with::

   mamba update mgkit

To create a new environment, run:

mamba create --name myenvname mgkit

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/mgkit:<tag>

(see `mgkit/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/mgkit/README.html)