1 Quick Start
A brief guide to setting up BiocMAP. A more detailed and thorough guide is here. For troubleshooting advice, see our guide.
1.1 Setup
- Clone the BiocMAP repository with
git clone git@github.com:LieberInstitute/BiocMAP.git - Change directory into the repository with
cd BiocMAP - Run the command
bash install_software.sh [option]to set up test files and software dependencies, where[option]must be replaced bydocker,singularity,conda,local, orjhpce. These respectively (and in descending order of our recommendation) correspond to using docker to manage software dependencies, using singularity, using conda, installing all software locally, or preparing BiocMAP for execution at the JHPCE cluster. - If using BiocMAP on a cluster, set the
arioc_queueArioc setting in your config file for the first module.
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, as well as which module you wish to run.
| Executor | Module | Script |
|---|---|---|
| SGE cluster | first | run_first_half_sge.sh |
| SGE cluster | second | run_second_half_sge.sh |
| SLURM cluster | first | run_first_half_slurm.sh |
| SLURM cluster | second | run_second_half_slurm.sh |
| local machine | first | run_first_half_local.sh |
| local machine | second | run_second_half_local.sh |
| The JHPCE cluster | first | run_first_half_jhpce.sh |
| The JHPCE cluster | second | run_second_half_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 combination of “executor” (SLURM cluster, SGE cluster, or local) and “module” (first half or second half) determine the name of your configuration file. Find your file under BiocMAP/conf/.
| Executor | Module | Config Filename |
|---|---|---|
| SGE cluster | first | first_half_sge.config |
| SGE cluster | second | second_half_sge.config |
| SLURM cluster | first | first_half_slurm.config |
| SLURM cluster | second | second_half_slurm.config |
| local machine | first | first_half_local.config |
| local machine | second | second_half_local.config |
| The JHPCE cluster | first | first_half_jhpce.config |
| The JHPCE cluster | second | second_half_jhpce.config |
As an example, suppose you have access to a SLURM cluster, and wish to run the second module to process existing alignments. Your config file is then BiocMAP/conf/second_half_slurm.config.