1 Quick Start
A brief guide to setting up SPEAQeasy. A more detailed and thorough guide is here.
- Clone the SPEAQeasy repository with
git clone email@example.com:LieberInstitute/SPEAQeasy.git
- Change directory into the repository with
- Users of the JHPCE cluster should run
bash install_software.sh "jhpce". All other users are recommended to run
bash install_software.sh "docker"or
bash 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 with
bash install_software.sh "local".
Note: JHPCE users must also make an edit to their
~/.bashrc files, described here
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.
|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
qsub). On local machines, the pipeline can be run interactively (i.e.
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
|The JHPCE cluster||jhpce.config|