Docs

Quick start – First steps

Creating an account
Connecting to the clusters
Introduction to Linux
Copying files
Editing files
Submitting jobs with Slurm
Glossary

Managing files

Disk space
Transferring files to and from the clusters
Using the common filesystem
Sharing files among CÉCI users
Copy files and folders to the /CECI/proj partition
Making your files Secure
Making your files safe
Long term data storage

Using software and libraries

Using pre-installed software
Software installed in the clusters
Compiling and installing software from source
Installing software by yourself
Singularity Container
Visualization server
Jupyter
Login shell

Submitting jobs to the cluster

Slurm F.A.Q
Slurm priorities
An interactive job submission tool: ssubmit
Getting Job Efficiency
Slurm limits
Workflow management
Slurm interactive jobs

Software-specific documentation

Matlab
R
Python

CÉCI

Docs »
GATK

GATK¶

Availability¶

Module	NIC5	Hercules2	Dragon2	Lemaitre3	Dragon1
GATK/4.1.4.1-GCCcore-8.3.0-Java-11	✓			✓
GATK/4.2.0.0-GCCcore-10.2.0-Java-1.8		✓

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