recipe cnasim

Improved simulation of single-cell copy number profiles and DNA-seq data from tumors

Homepage:

https://github.com/samsonweiner/CNAsim

License:

GPL-3.0-only

Recipe:

/cnasim/meta.yaml

CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. See our paper with the same name published in Bioinformatics.

package cnasim

(downloads) docker_cnasim

versions:

1.3.4-0

depends biopython:

>=1.8.1

depends dwgsim:

depends msprime:

>=1.2.0

depends numpy:

>=1.24.3

depends pyfaidx:

>=0.7.2.1

depends python:

>=3.7

depends samtools:

depends scipy:

>=1.10.1

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 cnasim

and update with::

   mamba update cnasim

To create a new environment, run:

mamba create --name myenvname cnasim

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/cnasim:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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