recipe svclone

Computational method for inferring cancer cell fraction of tumour SVs from WGS

Homepage:

https://github.com/mcmero/SVclone

License:

BSD / BSD-3-Clause

Recipe:

/svclone/meta.yaml

Links:

doi: 10.1038/s41467-020-14351-8

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.

package svclone

(downloads) docker_svclone

versions:

1.1.3-0,  1.1.2-1,  1.1.2-0,  1.1.1-0,  1.1.0-0,  v1.1.0-0

depends numpy:

depends pandas:

depends pysam:

depends python:

>=3

depends pyvcf:

depends r-base:

>=4.3,<4.4.0a0

depends r-ccube:

depends r-doparallel:

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 svclone

and update with::

   mamba update svclone

To create a new environment, run:

mamba create --name myenvname svclone

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/svclone:<tag>

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

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Link to this page

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