Package Recipe 'gubbins'

recipe gubbins

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

Homepage:: https://github.com/nickjcroucher/gubbins
Documentation:: https://nickjcroucher.github.io/gubbins
License:: GPL / GPL-2.0-or-later
Recipe:: /gubbins/meta.yaml
Links:: doi: 10.1093/nar/gku1196, biotools: gubbins, usegalaxy-eu: gubbins

package gubbins¶

Versions:

3.4.3-1, 3.4.3-0, 3.4.2-0, 3.4.1-0, 3.4-3, 3.4-2, 3.4-1, 3.4-0, 3.3.5-0,

3.4.3-1, 3.4.3-0, 3.4.2-0, 3.4.1-0, 3.4-3, 3.4-2, 3.4-1, 3.4-0, 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:

on bioconductor-ggtree
on bioconductor-treeio
on biopython
on dendropy >=5.0.8,<6.0a0
on fasttree >=2.1.10
on iqtree >=2.2,<3
on libgcc >=14
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on multiprocess
on numba
on numpy <=1.23.0
on numpy >=1.23.0,<2.0a0
on perl
on python >=3.10,<3.11.0a0
on python_abi 3.10.* *_cp310
on r-aplot
on r-argparser
on r-cowplot
on r-magrittr
on r-patchwork
on r-rcolorbrewer
on r-tidyverse
on rapidnj
on raxml >=8.2.12
on raxml-ng >=1.0.1
on scipy
on setuptools <82
on ska2 >=0.3.0
on veryfasttree

Additional platforms:

linux-aarch64, osx-arm64

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 gubbins

to add into an existing workspace instead, run:

pixi add gubbins

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 gubbins

Alternatively, to install into a new environment, run:

conda create -n envname gubbins

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/gubbins:<tag>

(see gubbins/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:

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