Package Recipe 'galaxy-data'

recipe galaxy-data

The Galaxy models, datatype framework, and datatype implementations.

Homepage:: https://galaxyproject.org
Documentation:: https://docs.galaxyproject.org
Developer docs:: https://github.com/galaxyproject/galaxy
License:: AFL-3.0
Recipe:: /galaxy-data/meta.yaml
Links:: biotools: galaxy, doi: 10.1093/nar/gky379

package galaxy-data¶

Versions:

25.1.2-0, 25.1.1-0, 25.0.4-0, 25.0.3-0, 25.0.2-0, 25.0.1-0, 24.2.4-0, 24.2.3-1, 24.2.3-0,

25.1.2-0, 25.1.1-0, 25.0.4-0, 25.0.3-0, 25.0.2-0, 25.0.1-0, 24.2.4-0, 24.2.3-1, 24.2.3-0, 24.2.2-0, 24.2.1-0, 24.2.0-0, 24.1.4-0, 24.1.3-0, 24.1.2-0, 24.1.1-0, 22.1.1-0, 21.9.0-0, 20.9.1-2, 20.9.1-1, 20.9.1-0

Depends:

on alembic
on alembic-utils
on bdbag >=1.6.3
on bx-python
on dnspython
on email-validator
on galaxy-files >=25.1
on galaxy-objectstore >=25.1
on galaxy-schema >=25.1
on galaxy-tool-util >=25.1
on galaxy-util >=25.1
on galaxy_sequence_utils
on h5grove >=1.2.1
on h5py
on isa-rwval >=0.10.10
on markupsafe
on mrcfile
on msal
on numpy
on parsley
on pycryptodome
on pydantic >=2.7.4
on pysam >=0.21
on python >=3.8
on python-isal
on python-magic
on rocrate
on social-auth-core 4.0.3
on sqlalchemy >=2.0,<2.1
on tifffile
on typing-extensions
on webob

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 galaxy-data

to add into an existing workspace instead, run:

pixi add galaxy-data

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 galaxy-data

Alternatively, to install into a new environment, run:

conda create -n envname galaxy-data

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/galaxy-data:<tag>

(see galaxy-data/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/galaxy-data/README.html)