recipe difcover

Pipeline to identify genomic regions with read coverage differences between pairs of samples

Homepage:

https://github.com/timnat/DifCover

License:

MIT

Recipe:

/difcover/meta.yaml

package difcover

versions:

3.0.1-1,  3.0.1-0

depends bedtools:

depends bioconductor-dnacopy:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends samtools:

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 difcover

and update with::

   mamba update difcover

To create a new environment, run:

mamba create --name myenvname difcover

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/difcover:<tag>

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

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