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:

3.4-1,  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, 

3.4-1,  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 bioconductor-ggtree:

depends bioconductor-treeio:

depends biopython:

depends dendropy:

>=5.0.1,<6.0a0

depends fasttree:

>2.1.10*

depends iqtree:

>=2.2

depends libgcc:

>=13

depends libzlib:

>=1.3.1,<2.0a0

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:

additional platforms:

linux-aarch64

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>``)

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