recipe augur

Process pathogen genome data for the Nextstrain platform

Homepage

https://github.com/nextstrain/augur

License

AGPL / AGPL-3.0

Recipe

/augur/meta.yaml

package augur

(downloads) docker_augur

Versions

5.1.0-0, 4.0.0-0, 3.1.5-1, 3.1.5-0

Depends bcbio-gff

0.6.*,>=0.6.4

Depends biopython

>=1.73

Depends boto

2.*,>2.38

Depends cvxopt

1.1.*,>=1.1.9

Depends fasttree

Depends ipdb

>=0.10.1

Depends iqtree

Depends jsonschema

3.0.0a3.*

Depends mafft

Depends matplotlib

2.*

Depends pandas

0.23.*,>=0.23.4

Depends python

>=3.4

Depends raxml

Depends seaborn

0.9.*,>=0.9.0

Depends snakemake

5.*,>=5.1.5

Depends treetime

0.5.*,>=0.5.2

Depends vcftools

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install augur

and update with:

conda update augur

or use the docker container:

docker pull quay.io/biocontainers/augur:<tag>

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