recipe poppunk

PopPUNK (POPulation Partitioning Using Nucleotide Kmers)

Homepage:

https://poppunk.bacpop.org

Documentation:

https://poppunk.bacpop.org/index.html

Developer docs:

https://github.com/bacpop/PopPUNK

License:

APACHE / Apache-2.0

Recipe:

/poppunk/meta.yaml

Links:

doi: 10.1101/gr.241455.118, biotools: poppunk

package poppunk

versions:

2.7.2-0,  2.7.1-0,  2.7.0-0,  2.6.7-0,  2.6.5-1,  2.6.5-0,  2.6.4-0,  2.6.3-0,  2.6.2-0, 

2.7.2-0,  2.7.1-0,  2.7.0-0,  2.6.7-0,  2.6.5-1,  2.6.5-0,  2.6.4-0,  2.6.3-0,  2.6.2-0,  2.6.1-0,  2.6.0-1,  2.6.0-0,  2.5.0-0,  2.4.0-2,  2.4.0-1,  2.4.0-0,  2.3.0-0,  2.2.0-0,  2.1.1-0,  2.0.2-0,  2.0.1-0,  1.2.2-0,  1.2.0-0,  1.1.7-0,  1.1.6-0,  1.1.5-0,  1.1.4-0,  1.1.3-0,  1.1.2-0

depends _openmp_mutex:

>=4.5

depends biopython:

depends dendropy:

>=4.4.0

depends graph-tool:

>=2.35

depends h5py:

depends hdbscan:

depends libgcc:

>=12

depends libgfortran:

depends libgfortran5:

>=12.4.0

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends mandrake:

depends matplotlib-base:

depends networkx:

depends numpy:

depends pandas:

depends pp-sketchlib:

>=2.0.1

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends rapidnj:

depends requests:

depends scikit-learn:

>=0.24

depends scipy:

depends tqdm:

depends treeswift:

depends xorg-libxaw:

depends xorg-libxcomposite:

depends xorg-libxcursor:

depends xorg-libxdamage:

depends xorg-libxfixes:

depends xorg-libxi:

depends xorg-libxinerama:

depends xorg-libxpm:

depends xorg-libxrandr:

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 poppunk

and update with::

   mamba update poppunk

To create a new environment, run:

mamba create --name myenvname poppunk

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/poppunk:<tag>

(see `poppunk/tags`_ for valid values for ``<tag>``)

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