recipe viroconstrictor

ViroConstrictor is a flexible pipeline for analysis of targeted viral sequencing data

Homepage:

https://rivm-bioinformatics.github.io/ViroConstrictor/

Developer docs:

https://github.com/RIVM-bioinformatics/ViroConstrictor

License:

AGPL / GNU Affero General Public v3

Recipe:

/viroconstrictor/meta.yaml

package viroconstrictor

versions:

1.4.2-0,  1.4.1-0,  1.4.0-1,  1.4.0-0,  1.3.1-0,  1.3.0-0,  1.2.6-0,  1.2.5-0,  1.2.4-0

depends aminoextract:

0.3.1

depends biopython:

>=1.79

depends conda:

depends drmaa:

0.7.9

depends fpdf2:

depends mamba:

depends openpyxl:

depends pandas:

>=1.5.1

depends python:

>=3.10

depends pyyaml:

6.0

depends rich:

13.*

depends snakemake:

>=7.15.2,<8

depends urllib3:

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 viroconstrictor

and update with::

   mamba update viroconstrictor

To create a new environment, run:

mamba create --name myenvname viroconstrictor

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/viroconstrictor:<tag>

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

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