Here contains various SLURM scripts to run for each step of the pipeline.
Most of the scripts are preformatted and ready to go except the email parameters to email you the results of the run.
To run most of the scripts, type in commands in this format:
sbatch test_pipeline.shWhen running the scripts found in the test/ directory, it will generate a
particular directory structure to ease of looking at results and intermediate
steps.
The file structure should look similar to the following.
root/
|-- data/
|-- intermediate/
|-- metadata/
|-- README.md
|-- results/
|-- slurm_submit.sh
`-- src/
5 directories, 2 files
You can run the following command on your local terminal to get plots or other data.
# Explanation:
# - scp - secure copy files
# - [email protected]:~/plots/plot-1.png - modify path after `:` for
# files you want to transfer
# - where/you/want/file.png - this is the path on your local instance
scp [email protected]:~/plots/plot-1.png where/you/want/file.png