bedtools

Singularity recipe and image

About bedtools

Logo

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Downloading the image from SyLabs.io

For simplicity, I have placed a copy of the container in SyLabs.io.

> singularity search bedtools

No users found for 'bedtools'

No collections found for 'bedtools'

Found 1 containers for 'bedtools'
	library://icaoberg/default/bedtools
		Tags: v2.29.2

To download this image locally simply run

singularity pull library://icaoberg/default/bedtools:v2.29.2

Using the Singularity image

Example. Create a master ChromHMM track from the 9 distinct cell types.

You can find the script example01 here. It is based on existing examples, the script is simply calling bedtools in the Singularity container.

Standard output is not neccesarily useful, however you should see something like this.

asciicast

Disclaimer

I am nothing but a humble programmer creating the container for this wonderful app. bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.