dockerbiotools/bedops repository overview

⁠bedops

bedops⁠ is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

⁠Building the Docker Container

To build the Docker container:

$ docker build -t dockerbiotools/bedops .

⁠Running bedops

You can run the fastStructure scripts like so:

$ docker run --rm --privileged -v /host/path:/data dockerbiotools/bedops tool arguments...

Since Docker containers have isolated file systems and changes to those filesystem do not persist between runs, you will need to mount a local directory inside the Docker container. To do so, replace /host/path with a local directory in the above command. Use the path /data in script arguments.

Available tools include:

• bam2bed
• bam2starch
• bedextract
• bedmap
• bedops
• closest-features
• convert2bed
• gff2bed
• gff2starch
• gtf2bed
• gtf2starch
• gvf2bed
• gvf2starch
• psl2bed
• psl2starch
• rmsk2bed
• rmsk2starch
• sam2bed
• sam2starch
• sort-bed
• starch
• starchcat
• unstarch
• vcf2bed
• vcf2starch
• wig2bed
• wig2starch