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) is a CBRS core facility that supports 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: 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 student21 , student22 .... We'll assign one to you.
The password for these accounts is written on the whiteboard.
These credentials are active for the next several days, but will be de-activated on Saturday May 20, 2023 in the evening.
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
Logging in
You 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.
ssh is an executable program that runs on your local computer and allows you to connect securely to a remote computer:
# 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
- 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
If you're attending remotely and do not have access to the UT VPN, you can use the Terminal functionality in the RStudio web application.
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=$LS_COLORS:'di=1;33:fi=01:ln=01;36'
In the RStudio Terminal, yellow is the default color for directories, which can be difficult to see against its white background. Execute this line to display directory names in blue.
export LS_COLORS=$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.