recipe atlas-metadata-validator

A MAGE-TAB validator for Expression Atlas and Single Cell Expression Atlas

Homepage:

https://github.com/ebi-gene-expression-group/atlas-metadata-validator

License:

APACHE / Apache Software

Recipe:

/atlas-metadata-validator/meta.yaml

This is a python module to parse a set of MAGE-TAB files and check for compatibility with the Expression Atlas and Single Cell Expression Atlas analysis pipelines. The main validation script automatically detects the experiment type from the MAGE-TAB and runs the respective tests. Currently general checks (for bulk and single-cell experiment) as well as Single Cell Expression Atlas specific checks are supported.

package atlas-metadata-validator

(downloads) docker_atlas-metadata-validator

versions:
1.6.1-0,  1.6.0-0,  1.5.0-0,  1.4.1-0,  1.4.0-0,  1.3.0-0,  1.2.1-0,  1.2.0-0,  1.1.0-0, 

1.6.1-0,  1.6.0-0,  1.5.0-0,  1.4.1-0,  1.4.0-0,  1.3.0-0,  1.2.1-0,  1.2.0-0,  1.1.0-0,  1.0.0-0

depends gitpython:

>=3.1.7

depends python:

>=3

depends requests:

>=2.20.1

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 atlas-metadata-validator

and update with::

   mamba update atlas-metadata-validator

To create a new environment, run:

mamba create --name myenvname atlas-metadata-validator

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/atlas-metadata-validator:<tag>

(see `atlas-metadata-validator/tags`_ for valid values for ``<tag>``)

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