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/v1.2.10/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:

1.2.10-0,  1.2.9H11-0

depends _openmp_mutex:

>=4.5

depends boost-cpp:

>=1.84

depends bzip2:

>=1.0.8,<2.0a0

depends gmp:

>=6.3.0,<7.0a0

depends libcurl:

>=8.14.1,<9.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends libgomp:

depends liblzma:

>=5.8.1,<6.0a0

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends openmpi:

>=4.1.6,<5.0a0

depends openssl:

>=3.5.2,<4.0a0

requirements:

additional platforms:

linux-aarch64

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 kled

and update with::

   mamba update kled

To create a new environment, run:

mamba create --name myenvname kled

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/kled:<tag>

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

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