Getting Started

Overview

About Anna

Anna is a member of the Center for Biomedical Research Support (CBRS), which is home to a number of core facilities: the Bioinformatics Consulting Group (BCG), Genome Sequencing and Analysis Facility (GSAF), Proteomics/Mass Spec, Microscopy, Mouse Genetic Engineering, and others.

Anna Battenhouse, Associate Research Scientist, abattenhouse@utexas.edu
- BA English literature, 1978, Carleton College
- Commercial software development 1982 – 2007
  - Texas Instruments, Motorola ...
  - lots of software development experience but limited Unix/Linux
- Joined Vishwanath Iyer Lab 2007 (functional genomics)
  - “retirement career”
  - began to appreciate Linux & bash (slowly)
- BS Biochemistry, 2013, UT
- Current affiliations:
  - Manager, Biomedical Research Computing Facility (BRCF)
  - member, Bioinformatics Consulting Group (BCG)
  - member, Marcotte lab (systems biology/proteomics)

The Biomedical Research Computing Facility (BRCF) and the Bioinformatics Consulting Group (BCG) are CBRS core facilities that support local research computing.

Note that Anna is not a Unix guru – there's a world of things she doesn't know! But she knows enough to be considered expert-ish

About you

Who has had command-line experience before? (E.g. Linux, Unix/Mac Unix, DOS)

What programming language experience do you have? (e.g. Python, R, Java)

Why use command-line Linux

See this section in the Intro Unix wiki: Getting Started#AboutUnix/Linux

The fundamental philosophy of Unix/Linux is to provide many small tools and utilities that can easily interact with each other using their built-in Input and Output streams.

The upside of this is that it affords tremendous flexibility, letting you perform complex data manipulations on the command line without writing a formal program or script.
The downside is that there are a lot of tools to learn, each with many options/switches.
- See Intro Unix: Some Linux commands for a gentle introduction to many useful Linux tools and some of their common options.

Setup to follow hands-on

This class is designed to be hands-on, to provide you with the enjoyment ( ) of working in the Linux command line environment.

However, all steps and scripts are detailed on this Wiki, and you will see me exercising processes on the command line interactively. So you may decide (at any time) to just watch and listen.

Note that you will have access to this Wiki even after the class, and I will email you a link to a video of the course.

If you choose to follow hands-on, you'll be using the BRCF "GSAF pod", a set of 3 compute servers attached to a large, shared storage server.

Accounts and servers

We have set up 99 "student" accounts, named student01 , student99 .... We'll assign one to you.

The password for these accounts is provided in the Chat.

These credentials are active for the next few weeks, but will be de-activated at the end of November.

With your studentNN account you can ssh into one of the following servers:

gsafcomp01.ccbb.utexas.edu – odd number studentNN accounts
gsafcomp02.ccbb.utexas.edu – even number studentNN accounts

UT VPN

For those associated with UT Austin and are not on the UT campus network, you'll need to have the UT VPN service active in order to connect to these servers via SSH. See How to Connect to the UT VPN

Folks not associated with UT Austin, or do not have the UT VPN service installed, can use an alternate web-based method, described below.

Logging in via SSH

You can access the servers using ssh in a Terminal program that runs on your computer. On Macs, this program is called Terminal. On Windows (Windows 10 or later) it is called Command Prompt or PowerShell. Find and open this program now on your computer.

Find ssh in Windows 10+

Windows versions 10 and later have the ssh program built in to their Command Prompt or PowerShell Terminals.

To open it, go to the Windows Start menu → Search for Command Prompt, then press Enter to open it.

ssh is an executable program that runs on your local computer and allows you to connect securely to a remote computer. We're going to use ssh to access one of the above compute servers on the GSAF pod:

# From the UT campus network, or if you have the UT VPN active:
ssh student02@gsafcomp02.ccbb.utexas.edu

Answer yes to the SSH security question prompt
- this will only be asked the 1st time you login
Enter the class password at the password prompt, then press Enter.
- for security reasons, the text that you enter will not be displayed

Once you've successfully logged in, you can logout by just typing exit then Enter. You'll then be back in your local computer's Terminal environment.

If your Windows version does not support ssh, you can download PuTTY from: https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html

Logging in with PuTTY

If you're using PuTTY as your Terminal from Windows:

Double-click the Putty icon
In the PuTTY Configuration window
- make sure the Connection type is SSH
- enter gsafcomp01.ccbb.utexas.edu for Host Name (or gsafcomp02.ccbb.utexas.edu)
  - Optional: to save this configuration for further use:
    - Enter gsafcomp into the Saved Sessions text box, then click Save
    - Next time select gsafcomp from the Saved Sessions list and click Load.
- click Open button
- answer Yes to the SSH security question
In the PuTTY Terminal
- enter your student account name after the "login as:" prompt, then Enter
- enter the password associated with our student accounts
  - for security reasons, the text that you enter will not be displayed

If your Terminal has a dark background, the default shell colors can be hard to read. Execute this line to display directory names in yellow.

export LS_COLORS=$LS_COLORS:'di=01;33:'

We'll see later how to set this environment variable in your login script (~/.profile) so that it gets executed every time you login to this server.

For now, just copy the appropriate line above, paste it into your Terminal window (after logging on), then press Enter.

Logging in via RStudio web

If you're attending remotely or do not have access to the UT VPN, you can use the Terminal functionality in the RStudio web application.

To access the Terminal built into RStudio Server.

Click on one of these links:
- https://gsafcomp01.ccbb.utexas.edu
- https://gsafcomp02.ccbb.utexas.edu
Select the RStudio link
Enter your studentNN account name and our password, then click the Sign In button
In the RStudio web application, select the Terminal tab above the type-in area

You should now see a command line in the RStudio type-in area.

In the RStudio Terminal if the default color for directories is difficult to see against its white background, execute this line to display directory names in blue.

export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'

We'll see later how to set this environment variable in your login script (~/.profile) so that it gets executed every time you login to this server.

For now, just copy the appropriate line above, paste it into your Terminal window (after logging on), then press Enter.