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.
Dorado
Dorado is a high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads.
Warning
Dorado requires a dependencies not available on CentOS 7. To make it run on stanage the team containerized the installation using Apptainer. As a result, Dorado is only recommended for use on single-node jobs. The container integration has been abstracted via the module system, allowing you to use Dorado as if it were a standard module.
Note: This is an experimental build. Please report any issues to the HPC support team.
Interactive Usage
After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:
srun --pty bash -i
#This will load the Dorado module and make the command available in your path.
module load dorado/1.0.1
# Run Dorado basecaller
dorado basecaller hac pod5s/ > calls.bam
Batch Submission
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --mem=5G
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=4
#Email notifications to me@somedomain.com
#SBATCH --mail-user=me@somedomain.com
#Email notifications if the job fails
#SBATCH --mail-type=FAIL
#SBATCH --job-name=dorado_test
module load dorado/1.0.1
dorado basecaller hac pod5s/ > calls.bam
Installation Notes
Dorado requires a newer version of GLIBC not available on the CentOS 7, so it is installed using Apptainer. The container definition file and easyconfig can be found here