recipe bedtk

Bedtk is a set of simple tools to process BED files.

Homepage:

https://github.com/lh3/bedtk

License:

MIT

Recipe:

/bedtk/meta.yaml

Links:

biotools: bedtk

Bedtk is a set of simple tools to process BED files. It so far implements intersection, subtraction, sorting, merging and computing the breadth of coverage. Bedtk is not as versatile as bedtools and never aims to match the bedtools feature set. It instead focuses on performance. Bedtk is several to tens of times faster and uses a fraction of memory. It also provides a few convenient functions. For example, sorting, merging and intersection can be done in one go without Unix pipes.

package bedtk

(downloads) docker_bedtk

versions:

0.0.r25.dirty-40.0.r25.dirty-30.0.r25.dirty-20.0.r25.dirty-10.0.r25.dirty-0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

requirements:

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 bedtk

and update with::

   mamba update bedtk

To create a new environment, run:

mamba create --name myenvname bedtk

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/bedtk:<tag>

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

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