Package Recipe 'skder'

recipe skder

skDER & CiDDER: efficient & high-resolution dereplication methods for microbial genomes

Homepage:: https://github.com/raufs/skDER
License:: BSD / BSD-3-Clause license
Recipe:: /skder/meta.yaml

package skder¶

Versions:

1.3.4-2, 1.3.4-1, 1.3.4-0, 1.3.3-0, 1.3.2-0, 1.3.1-1, 1.3.1-0, 1.3.0-0, 1.2.9-0,

1.3.4-2, 1.3.4-1, 1.3.4-0, 1.3.3-0, 1.3.2-0, 1.3.1-1, 1.3.1-0, 1.3.0-0, 1.2.9-0, 1.2.8-1, 1.2.8-0, 1.2.7-0, 1.2.6-0, 1.2.5-0, 1.2.4-0, 1.2.3-0, 1.2.2-0, 1.2.1-1, 1.2.1-0, 1.1.1-0, 1.0.10-0, 1.0.9-0, 1.0.8-0, 1.0.7-0, 1.0.6-0, 1.0.5-0, 1.0.4-0, 1.0.3-0, 1.0.1-1, 1.0.1-0, 1.0-0

Depends:

on aiofile
on aiohttp
on biopython
on cd-hit
on libgcc >=14
on libstdcxx >=14
on matplotlib-base
on pandas
on pyrodigal
on python >=3.10,<3.11.0a0
on python-igraph
on python_abi 3.10.* *_cp310
on seaborn
on setuptools
on skani
on tqdm
on wget

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 skder

to add into an existing workspace instead, run:

pixi add skder

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 skder

Alternatively, to install into a new environment, run:

conda create -n envname skder

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/skder:<tag>

(see skder/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/skder/README.html)