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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
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dockerbiotools
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