lab-10.md

tags
ggg, ggg2023, ggg298

Running workflows in multiple languages & using data analysis notebooks - GGG 298 - Week 10!

Setting things up on farm

We're using slightly different commands today -

So, ssh into farm and do an srun:

srun -p high2 --time=3:00:00 --nodes=1 \
    --cpus-per-task 4 --mem 10GB --pty /bin/bash

Activate the RStudio server module:

module load spack/R/4.1.1
module load rstudio-server/2022.12.0

Run rstudio-launch:

rstudio-launch

and follow the instructions to set up your ssh tunneling connection and log in to the RStudio Server.

Now clone and install the workflow!

Your first mission, should you choose to accept it:

Go to this repository and click "fork" (upper right).

Once that is completed, you will have a copy in your GitHub account!

Clone your copy of the repository into your farm account and run it.

Questions to be answered:

• what "human-readable" output files are created?
• what code/file creates compare.mat.png?
• what code/file/program creates compare.rstats.png?

Please do the following, in whatever order you like:

• change the color palette for the R script & pheatmap to use the 'inferno' palette;
• change output from png to pdf in R script;
• change output from png to pdf in the sourmash shell;
• add this genome and this genome into the workflow.

Run your new workflow, make sure it all works.

And now commit and push back to your fork.

TODO:

• add a few genomes