Attention
GPU users: GPU nodes run EL9, while this documentation still reflects the EL7 software stack.
Run module avail on an EL9 login node, or within an interactive session on the relevant GPU type, to see the software available.
The documentation will be updated once all nodes have migrated to EL9.
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 Stanage (see Establishing a SSH connection), start an interactive session with the following command:
srun --pty bash -i
The latest version of bedtools (currently version 2.31.0) is made available with the command:
module load BEDTools/2.31.0-GCC-12.3.0
After this any of the bedtools commands can be run from the prompt.
Installation notes
Bed tools was installed using EasyBuild/4.9.4, build details can be found in $EBROOTBEDTOOLS/easybuild with the module loaded.