recipe cyvcf2

A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files

Homepage:

https://github.com/brentp/cyvcf2/

Documentation:

https://brentp.github.io/cyvcf2/

License:

MIT / MIT

Recipe:

/cyvcf2/meta.yaml

Links:

doi: 10.1093/bioinformatics/btx057, biotools: cyvcf2

package cyvcf2

(downloads) docker_cyvcf2

versions:
0.30.28-1,  0.30.28-0,  0.30.27-0,  0.30.26-0,  0.30.25-0,  0.30.22-0,  0.30.16-2,  0.30.16-1,  0.30.16-0, 

0.30.28-1,  0.30.28-0,  0.30.27-0,  0.30.26-0,  0.30.25-0,  0.30.22-0,  0.30.16-2,  0.30.16-1,  0.30.16-0,  0.30.15-1,  0.30.15-0,  0.30.14-1,  0.30.14-0,  0.30.13-0,  0.30.12-0,  0.30.11-2,  0.30.11-1,  0.30.11-0,  0.30.9-0,  0.30.8-0,  0.30.6-1,  0.30.6-0,  0.30.4-0,  0.30.2-0,  0.30.1-0,  0.20.9-0,  0.20.8-0,  0.20.7-0,  0.20.6-0,  0.20.5-0,  0.20.4-1,  0.20.4-0,  0.20.3-0,  0.20.1-1,  0.20.1-0,  0.20.0-1,  0.20.0-0,  0.11.7-0,  0.11.6-0,  0.11.5-1,  0.11.5-0,  0.11.4-0,  0.11.2-0,  0.10.10-0,  0.10.8-2,  0.10.8-1,  0.10.8-0,  0.10.0-0,  0.8.4-4,  0.8.4-3,  0.8.4-2,  0.8.4-1,  0.8.4-0,  0.8.0-0,  0.7.2-3,  0.7.2-2,  0.7.2-1,  0.7.2-0,  0.6.6a-0,  0.6.5-0,  0.5.5-0,  0.5.3-0,  0.5.1-0,  0.5.0-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.2-0,  0.3.0-0,  0.2.8-0,  0.2.6-0,  0.2.5-0,  0.2.4-0,  0.2.3-0,  0.2.2-0,  0.2.0-0

depends click:

depends coloredlogs:

depends htslib:

>=1.19.1,<1.21.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends numpy:

>=1.21.6,<2.0a0

depends openssl:

>=3.2.1,<4.0a0

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

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 cyvcf2

and update with::

   mamba update cyvcf2

To create a new environment, run:

mamba create --name myenvname cyvcf2

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/cyvcf2:<tag>

(see `cyvcf2/tags`_ for valid values for ``<tag>``)

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