One time, you will need to set up a conda environment with R so that you have R available to run. After you have done this once, you can simply activate your existing environment as described below.

Do once: set up conda environment

After logging in to Hellgate, run

module load conda

so that the software conda is available to you.

Now you will create a conda environment to install R in. This one is called R_env; you could choose a different name if you want.

conda create -n R_env

You will then need to initiate conda so you can work with your new environment.

conda init bash

Now activate your new environment:

conda activate R_env

and install R:

conda install -c conda-forge r-base

Once this finishes, you should be able to open an interactive R session by running

R

and you can install devtools, stringdb, and our package as described on our package README. (Lucy note: I'm not sure how R manages these installations...they seem to persist across R sessions)

Activate environment and submit job

If you aren't already using the R_env, activate it:

conda activate R_env

Now you can run

sbatch submit_job.sh 

and check the status of your job with

squeue -u $USER

Output from your script will go to job_output_<jobid>.log and errors will go to job_error_<jobid>.log.