recipe vamb

Variational autoencoder for metagenomic binning.

Homepage:

https://github.com/RasmussenLab/vamb

Documentation:

https://vamb.readthedocs.io/en/latest

License:

MIT / MIT

Recipe:

/vamb/meta.yaml

Links:

doi: 10.1101/2024.10.25.620172, biotools: vamb

package vamb

versions:

5.0.3-0,  4.1.3-0,  3.0.2-2,  3.0.2-1,  3.0.2-0,  3.0.1-1,  3.0.1-0,  2.1.0-0,  2.0.1-0

depends dadaptation:

>=3.2

depends loguru:

>=0.7.0,<0.8

depends networkx:

>=3.4.2

depends numpy:

>=1.26.4,<3

depends pycoverm:

>=0.6.2

depends pyhmmer:

>=0.10.15

depends pyrodigal:

>=3.6.3

depends python:

>=3.10,<4

depends pytorch:

>=2.6.0

depends scikit-learn:

>=1.6.1

depends vambcore:

>=0.1.2,<0.2

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 vamb

and update with::

   mamba update vamb

To create a new environment, run:

mamba create --name myenvname vamb

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/vamb:<tag>

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

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