Package Recipe 'open-cravat'

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:

2.16.0-0, 2.15.0-0, 2.13.0-0, 2.12.0-0, 2.11.1-0, 2.11.0-0, 2.9.1-0, 2.9.0-0, 2.8.0-0,

2.16.0-0, 2.15.0-0, 2.13.0-0, 2.12.0-0, 2.11.1-0, 2.11.0-0, 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:

on aiohttp <4.0.0
on aiosqlite
on biopython
on chardet >=3.0.4
on intervaltree
on markdown
on mpmath
on nest-asyncio
on openpyxl
on oyaml
on psutil
on pyliftover
on python >=3.9
on pyvcf3
on pyyaml
on requests
on requests-toolbelt
on setuptools
on twobitreader
on websockets
on xlsxwriter

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install open-cravat

to add into an existing workspace instead, run:

pixi add open-cravat

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install open-cravat

Alternatively, to install into a new environment, run:

conda create -n envname open-cravat

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/open-cravat:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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/open-cravat/README.html)