About Us & About You
Your Instructor
Anna is a member of the Center for Biomedical Research Support (CBRS), which is home to a number of core facilities: GSAF, Proteomics/Mass Spec, Microscopy, Crystallography, Mouse Genetic Engineering....
- 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 Iyer Lab 2007 (functional genomics)
- “retirement career”
- began to appreciate Linux & bash (slowly)
- BS Biochemistry, 2013, UT
- Current affiliations:
- Biomedical Research Computing Facility (BRCF)
- Bioinformatics Consulting Group (BCG)
- Marcotte lab (proteomics)
The Biomedical Research Computing Facility (BRCF) is the CBRS core facility that supports local research computing.
About You
Tell us a bit about yourself, such as:
- your lab or organization
- research interests or staff role
- computational background, including any programming languages you use
- why you're interested in advanced bash scripting
Overview
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 as long as your UT EID is active, and a video of the course will also be posted on the home page.
Setup to follow hands-on
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
We have set up 50 "student" accounts, named student01 , student02 ... student50 . You have each been assigned one as follows, along with a server to use:
These credentials are active for the next few weeks, but will be de-activated at the end of the month (Sunday May 31, 2020).
Servers
With your studentNN account you can ssh into one of the following servers, according to the assignments above.
Remote server access requirements
Since you are attending this class remotely, you will need to use the UT VPN service or create a public/private key pair in order to access the shared compute environment.
How to set up a public/private key pair is cescribed here: POD Resources and Access#PasswordlessAccessviaSSH/SFTP. Once you have created the key pair, please email me the public key file (or its contents).
Once you have satisfied the remote access requirements, here's how to access the servers:
# If you have the UT VPN active: ssh student50@gsafcomp02.ccbb.utexas.edu # or, from outside the UT campus network, using public key encryption ssh -p 222 student50@gsafcomp02.ccbb.utexas.edu
Tip
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 (and put it in your ~/.profile login script)
export LS_COLORS=$LS_COLORS:'di=1;33:'
Desktop file browsing
Desktop file browsing is optional, but can come in handy for editing script files remotely.
You can connect your Mac or Windows laptop to your Home directory using the Samba network file system protocol. Once this is set up, you can use your favorite desktop code editing GUI to open, edit, and save files to your home directory.
Desktop file browsing using the Samba protocol is only available from the UT campus network so you will need to use the UT VPN service (described here: FAQ#HowtosetuptheUTVPNservice).
An alternative to Desktop file browsing is to use a text editor that has remote file editing capabilities using SSH (e.g. Komodo Edit, Sublime text edit (both Windows & Mac) and Notepad++ (Windows only).
Tip
Make sure you save script files with Unix/Linux line endings (linefeed only, not carriage_return + linefeed as is the Windows default).
On Windows
- Bring up Windows Explorer (e.g. Ctrl- <Windows key>)
- Select This PC → Computer tab → Map network drive
- In the Map Network Drive dialog box
- Select a drive letter (e.g. W: )
- In the Folder text box, enter: \\gsafstor01.ccbb.utexas.edu\users
- Check the Connect using different credentials checkbox
- Select Finish
- In the Enter network credentials dialog
- Enter your student account name and password AdvancedBash-Training
- Select OK
- You should now see a users (\\gsafstor01.ccbb.utexas.edu) (W:) item under This PC in Windows Explorer
On Macs
- Bring up the Finder
- Select Finder → Go → Connect to Server... (or just type ⌘-K )
- In the text box up top, enter: smb://gsafstor01.ccbb.utexas.edu/users
- Click on Connect
- Select Registered User
- Enter your student account name and password AdvancedBash-Training
- You should have a new window open with the contents of the Samba share. It will also be listed under Locations in the Finder sidebar