- recipe bedtk
Bedtk is a set of simple tools to process BED files.
- Homepage:
- License:
MIT / MIT
- Recipe:
- 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¶
- Versions:
1.2-0,1.1-0,0.0.r25.dirty-6,0.0.r25.dirty-5,0.0.r25.dirty-4,0.0.r25.dirty-3,0.0.r25.dirty-2,0.0.r25.dirty-1,0.0.r25.dirty-0- Depends:
on libgcc
>=13on libzlib
>=1.3.1,<2.0a0
- 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 bedtk
to add into an existing workspace instead, run:
pixi add bedtk
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 bedtk
Alternatively, to install into a new environment, run:
conda create -n envname bedtk
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/bedtk:<tag>
(see bedtk/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:
[](http://bioconda.github.io/recipes/bedtk/README.html)
