MARCC project manager for submitting CoGAPS runs

This repository contains a template for running multiple CoGAPS jobs on MARCC.

Setup

1. clone repository (change project_name to your project name)

git clone https://github.com/FertigLab/MARCC_SCRIPTS_FOR_COGAPS.git
mv MARCC_SCRIPTS_FOR_COGAPS project_name
cd project_name
chmod +x run

2. delete .git - you no longer need access to this repository

rm -rf .git

3. (optional) Create a new git repository to push your result to

git init
git add -A
git commit -m "first commit message"
git remote add origin https://github.com/username/new_repo
git push origin master

Your directory structure should now look like this (if you have tree installed you can see this with tree ..)

..
└── project_name
    ├── README.md
    ├── run
    └── scripts
        ├── job_script.sh
        └── R_script.R

Usage

Now that you have the directory structure set up, you can use the run script to submit jobs as follows:

1. modify the parameter values R_script.R for your specific case
2. modify the job parameters (i.e. #SBATCH ...) in job_script.sh
3. modify the modules in job_script.sh to specify version of R to use
4. execute ./run run_name run_id

This will copy over the scripts and run everything in a new directory called run_name/run_id. With these scripts you can quickly fire off multiple runs and all information (including log files) will be stored in a separate, well-structured directory.

Inside R_script.R and job_script.sh you can find instructions on how to modify those files.

For more information use ./run --help

Example

After modifying R_script.R and job_script.sh you might set off a few runs like this:

./run MySingleCellAnalysis 1

modify parameters again

./run MySingleCellAnalysis 2

and the result will be a directory like this:

├── MySingleCellAnalysis
│   ├── run_1
│   │   ├── logs
│   │   │   ├── slurm-31515407_1.out
│   │   │   ├── slurm-31515407_2.out
│   │   │   └── slurm-31515407_3.out
│   │   ├── result_1
│   │   │   └── sc_analysis_result.RData
│   │   ├── result_2
│   │   │   └── sc_analysis_result.RData
│   │   ├── result_3
│   │   │   └── sc_analysis_result.RData
│   │   └── scripts
│   │       ├── job_script.sh
│   │       └── R_script.R
│   └── run_2
│       ├── logs
│       │   ├── slurm-31558492_1.out
│       │   ├── slurm-31558492_2.out
│       ├── result_1
│       │   └── sc_analysis_result.RData
│       ├── result_2
│       │   └── sc_analysis_result.RData
│       └── scripts
│           ├── job_script.sh
│           └── R_script.R

The SLURM log files are sent to run_id/logs and the scripts used to set off the run are sent to run_id/scripts. All results are sent to run_id/result_id where the CogapsResult object is saved to an RData file. The number of results is determined by how many parameters are being looped over in R_script.R.

Bugs/Suggestions

Please let me know on Slack or at tomsherman159@gmail.com if there are any bugs in these scripts or if there any features you'd like to see added