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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
- Current 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.
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Note that you will have access to this Wiki even after the class as long as your UT EID is active, and I will email you a link to 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 75 "student" accounts, named student01 , student02 ... student50 student75 . You have each been assigned one as follows:
, along with a server to use:
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These credentials are active for the next few weeksdays, but will be de-activated at the end of the month (Sunday May on Monday October 31, 2020)2022. |
Servers
this With your studentNN account you can ssh into one of the following servers
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With this account you can ssh into one of the following servers, according to the assignments above:
- 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 you have the UT VPN active: ssh student50@gsafcomp02.ccbb.utexas.edu # or,The fromcommon outsidepassword thefor UTthese campusaccounts network,is usingposted publicin keythe encryption ssh -p 222 student50@gsafcomp02.ccbb.utexas.eduZoom 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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