recipe open-cravat

OpenCRAVAT - variant analysis toolkit

Homepage:

https://www.opencravat.org

Documentation:

https://github.com/KarchinLab/open-cravat/wiki

Developer docs:

https://github.com/KarchinLab/open-cravat

License:

MIT / MIT

Recipe:

/open-cravat/meta.yaml

package open-cravat

versions:

2.9.1-0,  2.9.0-0,  2.8.0-0,  2.7.3-0,  2.7.2-0,  2.7.1-0,  2.6.1-0,  2.6.0-0,  2.5.0-0, 

2.9.1-0,  2.9.0-0,  2.8.0-0,  2.7.3-0,  2.7.2-0,  2.7.1-0,  2.6.1-0,  2.6.0-0,  2.5.0-0,  2.4.2-0,  2.4.1-0,  2.4.0-0,  2.3.1-0,  2.3.0-0,  2.2.9-0,  2.2.7-0,  2.2.6-0,  2.2.5-0,  2.2.3-0,  2.2.2-0,  2.2.1-1,  2.2.1-0,  2.2.0-0,  2.1.2-0

depends aiohttp:

<4.0.0

depends aiosqlite:

depends biopython:

depends chardet:

>=3.0.4

depends intervaltree:

depends markdown:

depends mpmath:

depends nest-asyncio:

depends openpyxl:

depends oyaml:

depends psutil:

depends pyliftover:

depends python:

>=3.8

depends pyvcf3:

depends pyyaml:

depends requests:

depends requests-toolbelt:

depends twobitreader:

depends websockets:

depends xlsxwriter:

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 open-cravat

and update with::

   mamba update open-cravat

To create a new environment, run:

mamba create --name myenvname open-cravat

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/open-cravat:<tag>

(see `open-cravat/tags`_ for valid values for ``<tag>``)

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