recipe control-freec

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

Homepage:

https://github.com/BoevaLab/FREEC

License:

GPL2 / GPL-2.0-or-later

Recipe:

/control-freec/meta.yaml

Links:

biotools: freec

package control-freec

(downloads) docker_control-freec

Versions:
11.6-3,  11.6-2,  11.6-1,  11.6-0,  11.6b-3,  11.6b-2,  11.6b-1,  11.6b-0,  11.5-1, 

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

Depends:

  • on bioconductor-rtracklayer

  • on libgcc-ng >=12

  • on libstdcxx-ng >=12

  • on perl

  • on r-base

  • on samtools

Additional platforms:
linux-aarch64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install control-freec

to add into an existing workspace instead, run:

pixi add control-freec

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install control-freec

Alternatively, to install into a new environment, run:

conda create -n envname control-freec

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/control-freec:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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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