recipe oncocnv

a package to detect copy number changes in Deep Sequencing data

Homepage:

https://github.com/BoevaLab/ONCOCNV/blob/master/README.md

License:

GNU GPLv3

Recipe:

/oncocnv/meta.yaml

package oncocnv

versions:

7.0-2,  7.0-1,  7.0-0

depends bedtools:

>=2.27.1

depends bioconductor-dnacopy:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends r-base:

>=4.4,<4.5.0a0

depends r-digest:

depends r-fastica:

depends r-mass:

depends r-mclust:

depends r-pscbs:

depends r-remotes:

depends r-scales:

depends samtools:

>=1.16.1

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 oncocnv

and update with::

   mamba update oncocnv

To create a new environment, run:

mamba create --name myenvname oncocnv

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/oncocnv:<tag>

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

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