recipe contatester

Compute the Allelic Balance of a sample from a VCF file.

Homepage:

https://github.com/CNRGH/contatester

License:

CeCILL

Recipe:

/contatester/meta.yaml

Links:

biotools: contatester

Contatester computes the Allelic Balance of a sample from a VCF file, check if a cross human contamination is present and estimate the degree of contamination, using pegasus for high efficiency.

package contatester

versions:

1.0.0-2,  1.0.0-1,  1.0.0-0

depends bcftools:

>=1.9

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends openmpi:

>=4.1.5,<5.0a0

depends python:

>=3.10,<3.11.0a0

depends python-pegasus-wms:

>=4.8.2

depends python_abi:

3.10.* *_cp310

depends r-base:

>=4.2,<4.3.0a0

depends r-gridbase:

depends r-gridextra:

depends r-optparse:

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 contatester

and update with::

   mamba update contatester

To create a new environment, run:

mamba create --name myenvname contatester

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/contatester:<tag>

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

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