recipe gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

Homepage:

https://github.com/nickjcroucher/gubbins

License:

GPL-2.0

Recipe:

/gubbins/meta.yaml

package gubbins

Versions:

3.3.0-0,  3.3-0,  3.2.1-1,  3.2.1-0,  3.2.0-1,  3.2.0-0,  3.1.6-1,  3.1.6-0,  3.1.5-0, 

3.3.0-0,  3.3-0,  3.2.1-1,  3.2.1-0,  3.2.0-1,  3.2.0-0,  3.1.6-1,  3.1.6-0,  3.1.5-0,  3.1.4-0,  3.1.3-0,  3.1.2-0,  3.1.0-1,  3.1.0-0,  3.0.0-0,  2.4.1-2,  2.4.1-1,  2.4.1-0,  2.4.0-0,  2.3.5-0,  2.3.4-2,  2.3.4-1,  2.3.4-0,  2.3.2-0,  2.3.1-2,  2.3.1-1,  2.3.1-0,  2.2.1-0

Depends:

• biopython >=1.59

• dendropy >=4.0.2

• fasttree 2.1.10.*

• iqtree >=2.2

• libgcc-ng >=12

• libzlib >=1.2.13,<1.3.0a0

• multiprocess >=0.70

• numba >=0.56

• numpy >=1.2

• numpy >=1.23.0,<2.0a0

• perl >=5.32.1,<5.33.0a0 *_perl5

• python >=3.10,<3.11.0a0

• python_abi 3.10.* *_cp310

• rapidnj

• raxml 8.2.12.*

• raxml-ng 1.0.1.*

• reportlab >=3.0

• scipy >=1.5.3

• setuptools

• ska2

Required By:

• snpiphy

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install gubbins

and update with:

conda update gubbins

or use the docker container:

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

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gubbins/README.html)