- recipe gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
- Homepage:
- License:
GPL-2.0
- Recipe:
- package gubbins¶
- versions:
3.3.5-0
,3.3.4-1
,3.3.4-0
,3.3.3-1
,3.3.3-0
,3.3.1-0
,3.3.0-0
,3.3-0
,3.2.2-0
,3.3.5-0
,3.3.4-1
,3.3.4-0
,3.3.3-1
,3.3.3-0
,3.3.1-0
,3.3.0-0
,3.3-0
,3.2.2-0
,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 bioconductor-ggtree:
- depends bioconductor-treeio:
- depends biopython:
- depends dendropy:
- depends fasttree:
2.1.10.*
- depends iqtree:
>=2.2
- depends libgcc-ng:
>=12
- depends libzlib:
>=1.2.13,<1.3.0a0
- depends multiprocess:
- depends numba:
- depends numpy:
<=1.23.0
- depends numpy:
>=1.23.0,<2.0a0
- depends perl:
>=5.32.1,<5.33.0a0 *_perl5
- depends python:
>=3.9,<3.10.0a0
- depends python_abi:
3.9.* *_cp39
- depends r-aplot:
- depends r-argparser:
- depends r-cowplot:
- depends r-magrittr:
- depends r-patchwork:
- depends r-rcolorbrewer:
- depends r-tidyverse:
- depends rapidnj:
- depends raxml:
8.2.12.*
- depends raxml-ng:
1.0.1.*
- depends scipy:
- depends setuptools:
- depends ska2:
>=0.3.0
- 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 gubbins and update with:: mamba update gubbins
To create a new environment, run:
mamba create --name myenvname gubbins
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/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)