recipe control-freec

Copy number and genotype annotation from whole genome and whole exome sequencing data.

Homepage:

https://github.com/BoevaLab/FREEC

License:

GPL (>=2)

Recipe:

/control-freec/meta.yaml

Links:

biotools: freec

package control-freec

versions:

11.6-3,  11.6-2,  11.6-1,  11.6-0,  11.6b-0,  11.5-1,  11.5-0,  11.4-0,  10.6-0, 

11.6-3,  11.6-2,  11.6-1,  11.6-0,  11.6b-0,  11.5-1,  11.5-0,  11.4-0,  10.6-0,  10.5-0

depends bioconductor-rtracklayer:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends perl:

depends r-base:

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 control-freec

and update with::

   mamba update control-freec

To create a new environment, run:

mamba create --name myenvname control-freec

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/control-freec:<tag>

(see `control-freec/tags`_ for valid values for ``<tag>``)

Notes

The tool will be available as `freec` in the command line. See the homepage for example config files. Auxiliary scripts like e.g. freec2bed.pl and freec2circos.pl (see homepage) are available in the command line as well.

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