1 Quick Start

A brief guide to setting up SPEAQeasy. A more detailed and thorough guide is here.

1.1 Setup

  1. Clone the SPEAQeasy repository with git clone git@github.com:LieberInstitute/SPEAQeasy.git
  2. Change directory into the repository with cd SPEAQeasy
  3. 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 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