recipe vitap

Viral Taxonomic Assignment Pipeline

Homepage:

https://github.com/DrKaiyangZheng/VITAP/

Documentation:

https://github.com/DrKaiyangZheng/VITAP/blob/main/README.md

License:

GPL / GPL-3.0-only

Recipe:

/vitap/meta.yaml

Viral Taxonomic Assignment Pipeline (VITAP) is a cutting-edge tool designed to address the growing need for accurate and comprehensive taxonomic assignments of DNA and RNA viral sequences. By integrating alignment-based techniques with graph theory, VITAP achieves high precision in classifying viral sequences, including those as short as 1000 base pairs, down to the genus level.

package vitap

(downloads) docker_vitap

versions:

1.7-1,  1.7-0,  1.5-0,  1.2-0,  1.1-0

depends biopython:

>=1.78

depends diamond:

>=0.9

depends entrez-direct:

16.2.*

depends networkx:

>=3.1

depends numpy:

>=1.25

depends pandas:

>=1.5

depends prodigal:

>=2.6

depends python:

>=3.9

depends scipy:

>=1.10

depends seqkit:

>=2.5.1

depends tqdm:

>=4.65

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 vitap

and update with::

   mamba update vitap

To create a new environment, run:

mamba create --name myenvname vitap

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/vitap:<tag>

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

Download stats

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/vitap/README.html)