- recipe kipoi_veff
kipoi_veff: variant effect prediction plugin for Kipoi
- Homepage:
- Documentation:
- License:
MIT / MIT license
- Recipe:
kipoi_veff: variant effect prediction plugin for Kipoi
- package kipoi_veff¶
- Versions:
0.3.1-1,0.3.1-0,0.3.0-0,0.2.2-0,0.2.1-0,0.2.0-0,0.1.2-0- Depends:
on colorlog
on cookiecutter
on cyvcf2
on deepdish
on descartes
on future
on h5py
on intervaltree
on kipoi
>=0.5.5on kipoi-utils
on matplotlib
on numpy
on pandas
on pybedtools
on pysam
on python
on pyvcf
on seaborn
on shapely
on tqdm
on urllib3
>=1.21.1,<1.23
- 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 kipoi_veff
to add into an existing workspace instead, run:
pixi add kipoi_veff
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 kipoi_veff
Alternatively, to install into a new environment, run:
conda create -n envname kipoi_veff
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/kipoi_veff:<tag>
(see kipoi_veff/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/kipoi_veff/README.html)
