---
title: "Opening an RStudio instance in Klone"
author: "Kathleen Durkin"
date: "2025-02-19"
categories: ["misc"]
format:
  html:
    toc: true
    code-fold: true
engine: knitr
#bibliography: ../../../references.bib
---

## General instructions:

Open Cygwin (or other Unix tool)

```         
ssh kdurkin1@klone.hyak.uw.edu
```

Enter UW NetID password and complete the DUO prompt

Once I've accessed Klone, I'm in the `/mmfs1/home/kdurkin1` directory. All of the Roberts lab resources, however, are located in the `/gscratch/srlab/` directory

```         
cd /gscratch/srlab/
```

I have my own subdirectory, `/gscratch/srlab/kdurkin1`

To launch an RStudio server, run the .job file I have stored in my directory (edit if necessary using `nano`):

```         
cd /gscratch/srlab/kdurkin1
sbatch rstudio-server-ckpt.job
cat *.out
```

Open the output file, follow instructions by opening the directed ssh tunnel and signing in via NetID, then opening a webpage at the provided web address

## Resources

Potentially helpful commands:

`hyakalloc` : shows me what computational resources I have access to

`squeue | grep kdurkin1` : shows what jobs I have running

[Klone instructions (handbook)](https://robertslab.github.io/resources/klone_RStudio-Server/)\
[Video walkthrough](https://washington.zoom.us/rec/share/tM_4zmytAnDQrPoIxqDH0Q7RpaZviXcs9ih7ypUPSJCbaQc0Kwa6NnsqdeMvkvdF.P4qX95_arDgBeGMF)\
[My github issue troubleshooting this process](https://github.com/RobertsLab/resources/issues/2066)\
