- recipe biobb_adapters
Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.
- Homepage:
- License:
APACHE / Apache-2.0
- Recipe:
# biobb_adapters
### Introduction biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb_adapters.readthedocs.io/en/latest/).
### Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
- package biobb_adapters¶
- Versions:
5.1.2-0,5.1.1-0,5.1.0-0,4.0.0-0,3.8.1-0,3.8.0-0,3.7.0-0,3.6.1-0,3.6.0-0,5.1.2-0,5.1.1-0,5.1.0-0,4.0.0-0,3.8.1-0,3.8.0-0,3.7.0-0,3.6.1-0,3.6.0-0,0.1.4-0- Depends:
on python
>=3.9,<=3.12
- 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 biobb_adapters
to add into an existing workspace instead, run:
pixi add biobb_adapters
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 biobb_adapters
Alternatively, to install into a new environment, run:
conda create -n envname biobb_adapters
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/biobb_adapters:<tag>
(see biobb_adapters/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:
[](http://bioconda.github.io/recipes/biobb_adapters/README.html)
