Package Recipe 'kcftools'

recipe kcftools

Rapid method to screen for introgression using k-mer counting

Homepage:: https://github.com/sivasubramanics/kcftools
License:: GPL / GPL-3.0-only
Recipe:: /kcftools/meta.yaml

KCFTOOLS is a Java-based tool designed to identify genomic variations by analyzing k-mer counts between reference and query sequences. The tool leverages k-mer counting databases, such as those generated by KMC, to perform a variety of analyses, including variation detection, IBS window identification, and genotype matrix generation.

package kcftools¶

Versions:

0.4.0-0, 0.3.0-0, 0.2.0-0, 0.1.0-0, 0.0.1-0

Depends:

on kmc >=3.2.0
on openjdk 17.*
on python
on r-dplyr
on r-ggforce
on r-ggh4x
on r-ggplot2
on r-optparse
on r-svglite

Additional platforms:

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 kcftools

to add into an existing workspace instead, run:

pixi add kcftools

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 kcftools

Alternatively, to install into a new environment, run:

conda create -n envname kcftools

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/kcftools:<tag>

(see kcftools/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/kcftools/README.html)