Getting started with the I2BC cluster
Exercise summary
Introduction to cluster usage
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Objectives:
- first connection to the cluster
- understanding the file system (storage vs computing spaces)
- discovering cluster architecture & resources
- run your first interactive job
- learn where to find the software you need
- discover how to follow your storage quota & access backed up files on the cluster
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Objectives:
- learn how to create your first PBS submission script
- learn how to follow job progression
- analyse job resource consumption
- learn how to adapt the resources you ask for to your job requirements
- learn how to abort a job
- understand the concept of PBS queues
- play around with additional parameters for job submission and following
A few case studies to apply your knowledge
The following 3 exercises are guided exercises to help you apply what you’ve just learnt. They are all quite similar and vary just by the data and software that is used. Pick the one that your are most familiar with.
Tip: If you already have an advanced level, you can skim through case study 3, which finishes on a new concept: job arrays.
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Objectives: using the knowledge that you just acquired to run the FastQC software on some RNA-seq data
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Objectives: using the knowledge that you just acquired to run the Mafft software on some protein fasta sequences
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Objectives: using the knowledge that you just acquired to run the TMalign software on some protein structures
To go further
Tip: If you already have an advanced level, you can skim through case study 3, which finishes on a new concept: job arrays.