Running staarpipeline docker image

[pthami07]

Hi Xihaoli, Thanks for this seemingly great tool, I’d like to try it out. I’m having challenges with installing the staarpipeline dependencies. I’ve now pulled the docker image into an HPC as a singularity image. How do I run the image with the Rscripts that you have provided on GitHub?

[xihaoli]

Hi @pthami07,

Thanks for your interest in STAARpipeline. For the usage of docker as a singularity image file (sif), below are some example scripts for Slurm Workload Manager:

### Example 1: use sif to run an interactive R
salloc -p test -n 1 -t 00-08:00 --mem=6000 singularity shell staarpipeline_0.9.6.sif
R

### Example 2: use sif to run a single R script
salloc -p test -n 1 -t 00-08:00 --mem=6000 singularity shell staarpipeline_0.9.6.sif
R CMD BATCH Association_Analysis_PreStep.r

### Example 3: use sif in batch jobs
sbatch STAARpipeline_Gene_Centric_Coding.sh STAARpipeline_Gene_Centric_Coding.r

Note: In STAARpipeline_Gene_Centric_Coding.sh of Example 3, change /n/.../Rscript to singularity exec staarpipeline_0.9.6.sif Rscript

Best, Xihao