recipe augur

Process pathogen genome data for the Nextstrain platform.

Homepage:

https://github.com/nextstrain/augur

Documentation:

https://docs.nextstrain.org/projects/augur

License:

AGPL / AGPL-3.0-only

Recipe:

/augur/meta.yaml

Links:

doi: 10.21105/joss.02906, biotools: Augur

package augur

(downloads) docker_augur

versions:
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, 

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 bcbio-gff:

>=0.7.1,<0.8

depends biopython:

>=1.80,<2

depends cvxopt:

>=1.1.9,<2

depends fasttree:

depends iqtree:

depends isodate:

>=0.6.0,<0.7

depends jsonschema:

>=3.0.0,<4

depends mafft:

depends networkx:

>=2.5,<4

depends numpy:

>=1.0.0,<2

depends packaging:

>=19.2

depends pandas:

>=1.0.0,<2

depends pyfastx:

>=1.0.0,<3

depends python:

>=3.8

depends python-calamine:

>=0.2.0

depends raxml:

depends scipy:

>=1.0.0,<2

depends treetime:

>=0.11.2,<0.12

depends vcftools:

depends xopen:

>=1.7.0,<3

requirements:

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 augur

and update with::

   mamba update augur

To create a new environment, run:

mamba create --name myenvname augur

with myenvname being 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/augur:<tag>

(see `augur/tags`_ for valid values for ``<tag>``)

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