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:

2.0.5-0,  2.0.0-0

depends annotated-types:

0.6.0

depends certifi:

2023.7.22

depends charset-normalizer:

3.3.1

depends cyvcf2:

0.30.28

depends openpyxl:

3.1.2

depends pandas:

2.1.2

depends pydantic:

2.6.4

depends pymongo:

4.6.1

depends python:

>=3.10,<3.11.0a0

depends python-dateutil:

2.8.2

depends tqdm:

4.66.1

depends typing:

3.7.4.3

depends typing_extensions:

4.11.0

depends urllib3:

2.0.7

requirements:

additional platforms:

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 beacon2-ri-tools

and update with::

   mamba update beacon2-ri-tools

To create a new environment, run:

mamba create --name myenvname beacon2-ri-tools

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/beacon2-ri-tools:<tag>

(see `beacon2-ri-tools/tags`_ for valid values for ``<tag>``)

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