recipe vcontact3

Viral Contig Automatic Clustering and Taxonomy

Homepage:

https://bitbucket.org/MAVERICLab/vcontact3

Documentation:

https://bitbucket.org/MAVERICLab/vcontact3/src/master/README.md

License:

GPL / GPLv3

Recipe:

/vcontact3/meta.yaml

package vcontact3

(downloads) docker_vcontact3

versions:

3.0.0.b65-0,  3.0.0.b38-0

depends bioinfokit:

>=2.1.3

depends biopython:

>=1.81

depends dill:

>=0.3.6

depends ete3:

>=3.1.3

depends jenkspy:

>=0.3.2

depends jinja2:

>=3.0.3

depends joblib:

>=1.2.0

depends markupsafe:

>=2.0.1

depends matplotlib-base:

>=3.7.1

depends mmseqs2:

>=15.6f452

depends networkit:

>=11.0

depends networkx:

>=3.1

depends numpy:

>=1.23.5

depends pandas:

>=2.1.1

depends psutil:

>=5.9.5

depends pyarrow:

>=11.0.0

depends pyrodigal:

>=2.3.0

depends pyrodigal-gv:

>=0.3.1

depends pytables:

>=3.8.0

depends python:

>=3.9,<3.11

depends python-igraph:

>=0.10.4

depends scikit-bio:

>=0.5.8

depends scikit-learn:

>=1.2.2

depends scipy:

>=1.10.1

depends seaborn:

>=0.12.1

depends swifter:

>=1.3.4

depends tqdm:

>=4.65.0

depends upsetplot:

>=0.7.0

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 vcontact3

and update with::

   mamba update vcontact3

To create a new environment, run:

mamba create --name myenvname vcontact3

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/vcontact3:<tag>

(see `vcontact3/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/vcontact3/README.html)