recipe vcf2db

Create a gemini-compatible database from a VCF

Homepage:

https://github.com/quinlan-lab/vcf2db

License:

MIT

Recipe:

/vcf2db/meta.yaml

package vcf2db

(downloads) docker_vcf2db

versions:
2020.02.24-3,  2020.02.24-2,  2020.02.24-1,  2020.02.24-0,  2018.10.26-1,  2018.10.26-0,  2018.05.23-2,  2018.05.23-0,  2018.01.23-0, 

2020.02.24-3,  2020.02.24-2,  2020.02.24-1,  2020.02.24-0,  2018.10.26-1,  2018.10.26-0,  2018.05.23-2,  2018.05.23-0,  2018.01.23-0,  2017.12.11-0,  2017.11.15-0,  2017.10.11-0,  2017.09.14-0,  2017.04.12-0,  2017.03.01-0,  2017.02.25-0,  2017.02.24-1,  2017.02.24-0,  2017.01.10-0,  2016.12.09-1,  2016.12.09-0,  2016.11.08-0,  2016.04.29-0

depends cyvcf2:

>=0.30

depends geneimpacts:

>=0.3

depends nomkl:

depends numpy:

depends peddy:

>=0.2.9

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends python:

depends python-snappy:

depends snappy:

depends sqlalchemy:

<2.0

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 vcf2db

and update with::

   mamba update vcf2db

To create a new environment, run:

mamba create --name myenvname vcf2db

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/vcf2db:<tag>

(see `vcf2db/tags`_ for valid values for ``<tag>``)

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Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/vcf2db/README.html)