- recipe snakebids
BIDS integration into snakemake workflows
- Homepage:
- License:
MIT
- Recipe:
Snakebids is a Python package that extends Snakemake, enabling users to create reproducible, scalable pipelines for processing neuroimaging data in the BIDS format.
- package snakebids¶
- versions:
0.13.1-0- depends attrs:
>=22.2.0- depends boutiques:
>=0.5.25,<0.6.0- depends copier:
>=9.2.0- depends docutils:
!=0.21.post1- depends importlib-resources:
>=5.12.0- depends jinja2-time:
>=0.2.0- depends lazy-loader:
>=0.3- depends more-itertools:
>=8- depends numpy:
>=1.23.2- depends pluggy:
>=1.3- depends pvandyken-deprecated:
0.0.4- depends pybids:
>=0.16.0,<0.17- depends python:
>=3.8,<4.0- depends requests:
>=2.31.0- depends scipy:
>=1.10.0- depends snakemake:
>=7.18.2- depends typing_extensions:
>=3.10.0- 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 snakebids and update with:: mamba update snakebids
To create a new environment, run:
mamba create --name myenvname snakebids
with
myenvnamebeing 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/snakebids:<tag> (see `snakebids/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/snakebids/README.html)
