Package Recipe 'beacon2-ri-tools'

recipe beacon2-ri-tools

Package of tools designed to simplify the population of a Beacon v2 mongoDB database

Homepage:: https://github.com/EGA-archive/beacon2-ri-tools-v2/tree/main
License:: Apache-2.0
Recipe:: /beacon2-ri-tools/meta.yaml

Beacon2 RI Tools v2 is a software created with the main goal of generating BFF data from .csv or .vcf (and probably more types of datafiles in the future). This is based on the first beacon ri tools. Currently, the supported input formats are VCF, CSV, and Phenopackets. These formats are converted to BFF (Beacon Friendly Format JSON, following Beacon v2 official specifications) and inserted into a Beacon database.

package beacon2-ri-tools¶

Versions:

2.0.6-0, 2.0.5-0, 2.0.0-0

Depends:

on annotated-types >=0.6.0
on certifi >=2023.7.22
on charset-normalizer >=3.3.1
on coverage >=7.6.0
on cyvcf2 >=0.30.28
on openpyxl >=3.1.2
on pandas >=2.1.2
on pydantic >=2.6.4
on pydantic-core >=2.16.3
on pymongo >=4.6.1
on python >=3.10,<3.11.0a0
on python-dateutil >=2.8.2
on rfc3339-validator >=0.1.4
on tqdm >=4.66.1
on typing >=3.7.4.3
on typing_extensions >=4.11.0
on urllib3 >=2.0.7

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 beacon2-ri-tools

to add into an existing workspace instead, run:

pixi add beacon2-ri-tools

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 beacon2-ri-tools

Alternatively, to install into a new environment, run:

conda create -n envname beacon2-ri-tools

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/beacon2-ri-tools:<tag>

(see beacon2-ri-tools/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/beacon2-ri-tools/README.html)