recipe vcfsim

Script for generating simulated VCF's leveraging a coalescent simulating backend.

Homepage:

https://github.com/Pie115/VCFSimulator-SamukLab

License:

MIT

Recipe:

/vcfsim/meta.yaml

"VCFSim is a new command-line tool for generating simulated VCF's(variant call format files for encoding genetic data). Leveraging a coalescent simulating backend and providing an interface from Msprime coalescent simulating package to pandas. VCF's can now be easily simulated with just a few command line arguments!"

package vcfsim

(downloads) docker_vcfsim

versions:

1.0.11.alpha-0,  1.0.10.alpha-0,  1.0.9.alpha-0,  1.0.8.alpha-0

depends ipython:

depends msprime:

depends numpy:

depends pandas:

depends python:

>=3.6

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 vcfsim

and update with::

   mamba update vcfsim

To create a new environment, run:

mamba create --name myenvname vcfsim

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/vcfsim:<tag>

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

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Link to this page

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