ntd-cluster-example/README.md

In OxfordRSE/NTDMC_trachoma_pipeline: What the Package Does (One Line, Title Case)

Installation

1. Load required modules

module load gnu7 R python

1. Install pipeline package and AMIS package

devtools::install_github("OxfordRSE/trachomAMIS")
devtools::install_github("OxfordRSE/NTDMC_trachoma_pipeline")

1. Clone trachoma and install Python model

git clone https://github.com/ArtRabbitStudio/ntd-model-trachoma.git
python3 -m pip install ntd-model-trachoma/

Running the pipeline

1. Make sure you're happy with the parameters in input.yaml
2. Submit jobs with

sbatch batch.sh

Overview

Submission script submits a range of jobs to SLURM. Each job run the R script run_pipeline.R. Script run_pipeline.R loads the pipeline package and executes the trachoma pipeline for this particular job.

OxfordRSE/NTDMC_trachoma_pipeline documentation built on Dec. 18, 2021, 5:42 a.m.