Attention

ShARC will be decommissioned on the 30th of November 2023, after which time users will no longer be able to access that cluster and any jobs running or queueing at that time will be cancelled.

Please see our page of important info about ShARC’s decommissioning.

Bedtools

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Interactive usage

After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the srun --pty bash -i command.

The latest version of bedtools (currently version 2.29.2) is made available with the command:

module load BEDTools/2.29.2-GCC-9.3.0

After this any of the bedtools commands can be run from the prompt.

Installation notes

Bedtools was installed using Easybuild 4.3.1, build details can be found in /usr/local/packages/live/eb/BEDTools/2.29.2-GCC-9.3.0/easybuild/

Testing

See: https://github.com/rcgsheffield/sheffield_hpc/issues/1157

Modulefile

The module file is on the system at /usr/local/modulefiles/live/eb/all/BEDTools/2.29.2-GCC-9.3.0.