Package Recipe 'oakvar'

recipe oakvar

OakVar - Genomic Variant Analysis Platform

Homepage:: https://github.com/rkimoakbioinformatics/oakvar
Documentation:: https://rkimoakbioinformatics.github.io/oakvar
License:: AGPL / AGPL-3.0-or-later
Recipe:: /oakvar/meta.yaml
Links:: biotools: oakvar

package oakvar¶

Versions:

2.13.0-0, 2.12.25-0, 2.12.24-0, 2.12.23-0, 2.12.22-0, 2.12.21-0, 2.12.20-0, 2.12.19-0, 2.12.18-0,

2.13.0-0, 2.12.25-0, 2.12.24-0, 2.12.23-0, 2.12.22-0, 2.12.21-0, 2.12.20-0, 2.12.19-0, 2.12.18-0, 2.12.17-0, 2.12.15-0, 2.12.12-0, 2.12.11-0, 2.12.10-0, 2.12.9-0, 2.12.7-0, 2.12.6-0, 2.12.5-0, 2.12.4-0, 2.12.3-0, 2.12.2-0, 2.11.26-0, 2.11.25-0, 2.11.24-0, 2.11.21-0, 2.11.14-0, 2.11.11-0, 2.11.10-0, 2.11.9-0, 2.11.8-0, 2.11.5-0, 2.11.4-0, 2.11.3-0, 2.11.2-0, 2.11.1-0, 2.11.0-0, 2.10.4-0, 2.10.3-0, 2.10.2-0, 2.10.1-0, 2.9.128-0, 2.9.127-0, 2.9.123-0, 2.9.122-0, 2.9.119-0, 2.9.116-0, 2.9.114-0, 2.9.112-0, 2.9.111-0, 2.9.110-0, 2.9.109-0, 2.9.106-0, 2.9.97-0, 2.9.96-0, 2.9.95-0, 2.9.94-0, 2.9.93-0, 2.9.92-0, 2.9.91-0, 2.9.90-0, 2.9.89-0, 2.9.88-0, 2.9.87-0, 2.9.85-0, 2.9.83-0, 2.9.82-0, 2.9.81-0, 2.9.80-0, 2.9.78-0, 2.9.77-0, 2.9.75-0, 2.9.72-0, 2.9.71-0, 2.9.69-0, 2.9.68-0, 2.9.64-0, 2.9.62-0, 2.9.60-0, 2.9.59-0, 2.9.58-0, 2.9.57-0, 2.9.56-0, 2.9.55-0, 2.9.54-0, 2.9.53-0, 2.9.52-0, 2.9.51-0, 2.9.49-0, 2.9.43-0, 2.9.41-0, 2.9.39-0, 2.9.37-0, 2.9.36-0, 2.9.34-0, 2.9.3-0, 2.9.2-0, 2.9.1-0, 2.8.40-0, 2.8.38-0, 2.8.37-0, 2.8.36-0, 2.8.35-0, 2.8.28-0, 2.7.40-0

Depends:

on aiohttp <4.0.0
on aiohttp-cors
on aiosqlite
on chardet >=3.0.4
on connectorx
on download
on duckdb
on gdown
on intervaltree
on liftover
on markdown
on mpmath
on multiprocess
on nest-asyncio
on oyaml
on packaging
on pillow
on polars
on psutil
on pyarrow
on pyjwt
on pysimplegui
on python >=3.8
on python-dateutil
on requests
on requests-toolbelt
on rich
on split-file-reader
on twobitreader
on ujson

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 oakvar

to add into an existing workspace instead, run:

pixi add oakvar

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 oakvar

Alternatively, to install into a new environment, run:

conda create -n envname oakvar

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/oakvar:<tag>

(see oakvar/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/oakvar/README.html)