Package Recipe 'poppunk'

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:

2.7.8-0, 2.7.7-0, 2.7.6-0, 2.7.5-0, 2.7.2-2, 2.7.2-1, 2.7.2-0, 2.7.1-0, 2.7.0-0,

2.7.8-0, 2.7.7-0, 2.7.6-0, 2.7.5-0, 2.7.2-2, 2.7.2-1, 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:

on _openmp_mutex >=4.5
on biopython
on dendropy >=4.4.0
on graph-tool >=2.35
on h5py
on hdbscan
on libgcc >=13
on libgfortran
on libgfortran5 >=13.4.0
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on mandrake
on matplotlib-base
on networkx
on numpy
on pandas
on pp-sketchlib >=2.0.1
on python >=3.10,<3.11.0a0
on python_abi 3.10.* *_cp310
on rapidnj
on requests
on scikit-learn >=0.24
on scipy
on tqdm
on treeswift
on xorg-libxaw
on xorg-libxcomposite
on xorg-libxcursor
on xorg-libxdamage
on xorg-libxfixes
on xorg-libxi
on xorg-libxinerama
on xorg-libxpm
on xorg-libxrandr

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 poppunk

to add into an existing workspace instead, run:

pixi add poppunk

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 poppunk

Alternatively, to install into a new environment, run:

conda create -n envname poppunk

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/poppunk:<tag>

(see poppunk/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/poppunk/README.html)