trapnell-cluster

This repository contains common scripts one might use while working on Nexus.

Installation

On your own computer

Edit your ~/.ssh/config file to contain the following:

Host *.gs.washington.edu
    User <your-GS-username-here>
    EnableEscapeCommandline yes

On Nexus

Run:

./install.sh

This will create the following directories in $HOME, if they do not exist already:

• bin: executable scripts
• sge: scripts that get submitted as jobs
• nobackup/log: a place for logfiles

Additionally, it will add $HOME/bin to your $PATH if it is not already present.

Usage

Currently this repo only contains a script to submit a VSCode server that can be run remotely. To use it, simply type serve_vscode. Additional usage details are available by running serve_vscode -h. To use VSCode remotely, you will also have to install the Remote Development Extension Pack. Read how to set up you local VS Code instance to connect to a Remote Tunnel here. You'll also probably want to set it up for R Development.

Contributing

If you would like to contribute modifications or additional cluster helpers, please create a branch and open a pull request for an admin to review.