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:

  • on gitpython >=3.1.7

  • on python >=3

  • on requests >=2.20.1

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 atlas-metadata-validator

to add into an existing workspace instead, run:

pixi add atlas-metadata-validator

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 atlas-metadata-validator

Alternatively, to install into a new environment, run:

conda create -n envname atlas-metadata-validator

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/atlas-metadata-validator:<tag>

(see atlas-metadata-validator/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 install-with-bioconda 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/atlas-metadata-validator/README.html)