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About
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Your Instructor
Anna
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
- Affiliations as of summer 2017Current affiliations:
- Biomedical Research Computing Facility (BRCF)
- Bioinformatics Consulting Group (BCG)
- Genome Sequencing and Analysis Facility (GSAF)
- Marcotte lab (systems biology/proteomics)
The Biomedical Research Computing Facility (BRCF) is the CBRS core facility that supports local research computing.
...
- Claire McWhite, claire.mcwhite@utexas.edu
5th year graduate student in the Marcotte Lab
- Research Interests: Proteomics, protein-protein interactions, networks
- Comparative biology
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, and I will email you a link to a video of the course.
Setup
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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 75 "student" accounts, named student01 , student02 ... student50 student75 . You have each been assigned one ...The super-secret password for all these accounts is: AdvancedBash-Trainingas follows, along with a server to use:
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These credentials are active for the next few days, but will be de-activated at the end of this week (Friday August 23)on Monday October 31, 2022. |
Servers
With this your studentNN account you can ssh into one of the following servers (please divide yourselves among them):
- gsafcomp01.ccbb.utexas.edu
- gsafcomp02.ccbb.utexas.edu
- gsafcbig01.ccbb.utexas.edu
For example:
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, according to the assignments given.
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Here's how to access the servers:
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# From the UT campus network, or if usingyou publichave keythe encryptionUT sshVPN -pactive: 222ssh student50@gsafcomp02.ccbb.utexas.edu | ||
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If 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
# The common password for these accounts is posted in the Zoom chat. |
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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)
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Desktop file browsing
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.
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Desktop file browsing using the Samba protocol is only available from the UT campus network. If you are attending this class remotely, 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). |
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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
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