1 Quick Start
A brief guide to setting up SPEAQeasy. A more detailed and thorough guide is here.
1.1 Setup
- Clone the SPEAQeasy repository with
git clone git@github.com:LieberInstitute/SPEAQeasy.git - Change directory into the repository with
cd SPEAQeasy - Users of the JHPCE cluster should run
bash install_software.sh "jhpce". All other users are recommended to runbash install_software.sh "docker"orbash install_software.sh "singularity", to use either docker or singularity to manage software, respectively. This will install nextflow and set up some test files. Otherwise, you can install everything required locally withbash install_software.sh "local".
Note: JHPCE users must also make an edit to their ~/.bashrc files, described here
1.2 Configuration
1.2.1 Your “main” script
The script you will use to run the pipeline depends on the system (“executor”) you wish to run the pipeline on.
| Executor | Script |
|---|---|
| SGE cluster | run_pipeline_sge.sh |
| SLURM cluster | run_pipeline_slurm.sh |
| local machine | run_pipeline_local.sh |
| The JHPCE cluster | run_pipeline_jhpce.sh |
Options included in the main script should be modified as appropriate for the experiment. On SLURM and SGE clusters (including JHPCE), the main script should be submitted as a job (i.e. using sbatch or qsub). On local machines, the pipeline can be run interactively (i.e. bash run_pipeline_local.sh).
1.2.2 Your config file
Your “executor” (SLURM cluster, SGE cluster, or local) determines the name of your config, regardless of how you choose to install SPEAQeasy. Find your file under SPEAQeasy/conf/.
| Executor | Config Filename |
|---|---|
| SGE cluster | sge.config |
| SLURM cluster | slurm.config |
| local machine | local.config |
| The JHPCE cluster | jhpce.config |