- recipe augur
Process pathogen genome data for the Nextstrain platform.
- Homepage:
- Documentation:
- License:
AGPL / AGPL-3.0-only
- Recipe:
- Links:
doi: 10.21105/joss.02906, biotools: Augur
- package augur¶
- Versions:
33.0.1-0,33.0.0-0,32.1.0-0,32.0.0-0,31.5.0-0,31.4.0-0,31.3.0-0,31.2.1-0,31.2.0-1,33.0.1-0,33.0.0-0,32.1.0-0,32.0.0-0,31.5.0-0,31.4.0-0,31.3.0-0,31.2.1-0,31.2.0-1,31.2.0-0,31.1.0-0,31.0.0-0,30.0.1-0,30.0.0-0,29.1.0-0,29.0.0-0,28.0.1-0,28.0.0-0,27.2.0-0,27.1.0-0,27.0.0-0,26.2.0-1,26.2.0-0,26.1.0-0,26.0.0-0,25.4.0-0,25.3.0-0,25.2.0-0,25.1.1-0,25.1.0-0,25.0.0-0,24.4.0-1,24.4.0-0,24.3.0-0,24.2.3-0,24.2.2-0,24.2.1-0,24.2.0-0,24.1.0-0,24.0.0-0,23.1.1-1,23.1.1-0,23.1.0-0,23.0.0-0,22.4.0-0,22.3.0-0,22.2.0-0,22.1.0-0,22.0.3-0,22.0.2-0,22.0.1-0,22.0.0-0,21.1.0-0,21.0.1-1,21.0.1-0,21.0.0-1,21.0.0-0,20.0.0-0,19.3.0-0,19.2.0-0,19.1.0-0,19.0.0-0,18.2.0-0,18.1.2-0,18.1.1-0,18.1.0-0,18.0.0-0,17.1.0-1,17.1.0-0,17.0.0-1,17.0.0-0,16.0.3-0,16.0.2-0,16.0.1-0,15.0.2-0,15.0.1-0,15.0.0-0,14.1.0-0,14.0.0-0,13.1.2-0,13.1.1-0,13.1.0-0,13.0.4-0,13.0.3-0,13.0.2-0,13.0.1-1,13.0.1-0,13.0.0-0,12.1.1-0,12.0.0-0,11.3.0-0,11.2.0-1,11.2.0-0,11.1.2-1,11.1.2-0,11.1.0-0,11.0.0-0,10.3.0-0,10.2.0-0,10.1.1-0,10.1.0-0,10.0.4-0,10.0.3-0,10.0.2-0,10.0.0-1,10.0.0-0,9.0.0-1,9.0.0-0,8.0.0-0,7.0.2-0,6.4.3-0,6.4.2-0,6.4.1-0,6.4.0-0,6.3.0-0,6.2.0-0,6.1.1-0,6.1.0-0,6.0.0-0,5.4.1-0,5.4.0-0,5.3.0-0,5.2.1-0,5.2.0-0,5.1.1-0,5.1.0-0,4.0.0-0,3.1.5-1,3.1.5-0- Depends:
on bcbio-gff
>=0.7.1,<0.8on biopython
>=1.80,<2on cvxopt
>=1.1.9,<2on fasttree
on iqtree
on isodate
>=0.6.0,<0.8on jsonschema
>=4.18.0,<5on mafft
on networkx
>=2.5,<4on numpy
>=1.0.0,<3on packaging
>=19.2on pandas
>=1.4.0,<3on pyfastx
>=1.0.0,<3on python
>=3.10on python-calamine
>=0.2.0on pyyaml
on raxml
on referencing
>=0.29.1,<1on scipy
>=1.0.0,<2on seqkit
on sqlite
>=3.39,<4on treetime
>=0.11.2,<0.12on vcftools
on xopen
>=2.0.0,<3
- 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 augur
to add into an existing workspace instead, run:
pixi add augur
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 augur
Alternatively, to install into a new environment, run:
conda create -n envname augur
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/augur:<tag>
(see augur/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/augur/README.html)
