Overview

This is an introduction to the Unix Shell and High Performance Computing for members of the Helen Diller Family Comprehensive Cancer Center and the general cancer community.

Learning Objectives

• In Unix: Navigate the file system, manipulate files and directories, search for files with grep and find, write simple loops and scripts, and automate basic tasks.
• HPC objectives: Learn how to submit jobs to the TIPCC or Wynton clusters.

Prerequisites

There are no prerequisites, other than to have the software installed on your laptop prior to the workshop, and to have a TIPCC or Wynton cluster account (see below). Bring your laptop! Computers will not be provided.

Software

• Mac and Unix/Linux users: no installation necessary, or OS already has a unix shell
• Windows users: please install Git for Windows

Cluster Accounts

• Cancer Center members: you should already have a TIPCC account
• All others: you will need to request a Wynton account if you do not already have one. Note: new account requests will need to be made at least 2 weeks in advance of the workshop.

Materials

Unix materials available in the CLE: Introduction to Unix

Instructors

Geoffrey Boushey is a Software Developer in the UCSF Library's Data Science Initiative
Henrik Bengtsson, PhD, MS is an Associate Professor in the Deptartment of Epidemiology & Biostatistics
Karla Lindquist, PhD is the Scientific Lead for the UCSF Library's Data Science Initiative

Sponsors

Computational Biology and Informatics Shared Resource (http://cbi.ucsf.edu), the Bioinformatics Shared Resource, and the Library Data Science Initiative (library.ucsf.edu/data-science).