- recipe freyja
Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics.
- Homepage:
- Documentation:
- License:
BSD / BSD-2-Clause
- Recipe:
- Links:
biotools: freyja, usegalaxy-eu: freyja_demix, usegalaxy-eu: freyja_variants, usegalaxy-eu: freyja_boot, usegalaxy-eu: freyja_aggregate_plot
- package freyja¶
- Versions:
2.0.3-0,2.0.2-0,2.0.1-0,2.0.0-0,1.5.3-3,1.5.3-2,1.5.3-1,1.5.3-0,1.5.2-0,2.0.3-0,2.0.2-0,2.0.1-0,2.0.0-0,1.5.3-3,1.5.3-2,1.5.3-1,1.5.3-0,1.5.2-0,1.5.1-1,1.5.1-0,1.5.0-0,1.4.9-0,1.4.8-0,1.4.7-0,1.4.6-0,1.4.5-0,1.4.4-0,1.4.3-0,1.4.2-0,1.4.1-0,1.3.12-0,1.3.11-0,1.3.10-0,1.3.9-0,1.3.8-0,1.3.7-0,1.3.6-0,1.3.5-0,1.3.4-0,1.3.3-0,1.3.2-0,1.3.1-0,1.3-1,1.3-0,1.2.1-0,1.2-0,1.1-0- Depends:
on biopython
on click
on cvxpy
on epiweeks
on ivar
on joblib
on matplotlib-base
on numpy
on pandas
on plotly
on pyarrow
>=10.0.1on pysam
on python
>=3.7on pyyaml
on requests
on samtools
on seaborn-base
on sphinx
on sphinx-click
on sphinx_rtd_theme
on tqdm
on usher
- 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 freyja
to add into an existing workspace instead, run:
pixi add freyja
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 freyja
Alternatively, to install into a new environment, run:
conda create -n envname freyja
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/freyja:<tag>
(see freyja/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/freyja/README.html)
