Summary and Setup

This is a new lesson built with The Carpentries Workbench.

Data Sets

Download the data zip file and unzip it to your Desktop

Software Setup

Install Gcloud tools.

Open a Google Cloud SDK Shell window and run the following command:

gcloud compute ssh --zone "us-east1-b" "sumnergcp-controller" --tunnel-through-iap --project "jax-presgraves-edusumner2"

This will open another terminal window which will connect to the Google Cloud Platform (GCP).

Picture of slurm window open on GCP
GCP window with slurm prompt

Next, type the following command:

module load rstudio

This will produce the following message:

Rstudio 4.4.1 loaded. Use the command 'sbatch -w sumnergcp-computenodeset-1
rstudio-session.job' to start a new session on node 2. You can change the node
number if you want to run on a different node. The cluster has 30 compute nodes
ranging from 0 to 29

Follow the instructions in the message by typing the following command into the GCP window.

sbatch -w sumnergcp-computenodeset-1 rstudio-session.job

This will start a compute queue job which will be reported as:

Submitted batch job <N>

where is an integer that is your slurm job ID. The login node is spawning a compute node where RStudio will run.

After about two minutes, you should see a file like this in your home directory:

rstudio-server.job.<N>

where is the same integer as your batch job ID.

View the contents of the file using teh cat command:

cat rstudio-server.job.<N>

You will be instructions which tell you how to access your GCP RStudio instance along with a user name and password.

> cat rstudio-server.job.53
**********************************************************************
  RStudio server IP address: 35.196.22.80
  The name of the compute instance running the server is sumnergcp-computenodeset-1
***********************************************************************

Follow the instaructions below to connect to your
rstudio instance:

1. point your web browser to http://35.196.22.80:8787
2. log in to RStudio Server using the following credentials:

  user: dan_gatti_jax_org
  password: Dw7Qr3ejbOwBmtOPHxQt

When done using RStudio Server, terminate the job by:

1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
2. Issue the following command on the login node:

      scancel -f 53

Install R packages:

{r eval=FALSE} install.packages(c('BiocManager', 'remotes', 'tidyverse', 'qtl2'))

remotes::install_github('churchill-lab/intermediate')

Details

Setup for different systems can be presented in dropdown menus via a spoiler tag. They will join to this discussion block, so you can give a general overview of the software used in this lesson here and fill out the individual operating systems (and potentially add more, e.g. online setup) in the solutions blocks.

Use PuTTY

Use Terminal.app

Use Terminal