recipe vcf2genome

A tool to create a draft genome file out of a GATK VCF file and enabling users to filter the VCF in a single step.

Homepage:

https://github.com/apeltzer/vcf2genome

License:

GPLv3

Recipe:

/vcf2genome/meta.yaml

package vcf2genome

(downloads) docker_vcf2genome

versions:

0.91-2,  0.91-1,  0.91-0

depends openjdk:

depends python:

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 vcf2genome

and update with::

   mamba update vcf2genome

To create a new environment, run:

mamba create --name myenvname vcf2genome

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/vcf2genome:<tag>

(see `vcf2genome/tags`_ for valid values for ``<tag>``)

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Link to this page

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