Package Recipe 'kled'

recipe kled

An ultra-fast and sensitive structural variant detection tool for long-read sequencing data.

Homepage:: https://github.com/CoREse/kled
Documentation:: https://github.com/CoREse/kled/blob/v1.2.11/README.md
License:: MIT / MIT
Recipe:: /kled/meta.yaml
Links:: biotools: kled, doi: 10.1093/bib/bbae049, doi: 10.3389/fgene.2024.1435087

Kled is designed to call SVs nicely and quickly using long-read sequencing data. It takes mapped reads file (bam) as input and reports SVs to the stdout in the VCF file format. Kled can yield precise and comprehensive SV detection results within minutes and can run on any modern computer without needing of any field knowledge of the user to perform the SV detection.

package kled¶

Versions:

1.2.11-0, 1.2.10-0, 1.2.9H11-0

Depends:

on _openmp_mutex >=4.5
on boost-cpp >=1.84
on bzip2 >=1.0.8,<2.0a0
on gmp >=6.3.0,<7.0a0
on libcurl >=8.19.0,<9.0a0
on libdeflate >=1.25,<1.26.0a0
on libgcc >=14
on libgomp
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on openmpi >=4.1.6,<5.0a0
on openssl >=3.5.5,<4.0a0

Additional platforms:

linux-aarch64

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 kled

to add into an existing workspace instead, run:

pixi add kled

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 kled

Alternatively, to install into a new environment, run:

conda create -n envname kled

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/kled:<tag>

(see kled/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/kled/README.html)