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This page should serve as a reference for the many "things Linux" we use in this course. It is by no means complete – Linux is **huge** – but offers introductions to many important topics.

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  • Macs and Linux have a Terminal program built-in
  • Windows options:

Use ssh (secure shell) to login to a remote computers.

Code Block
languagebash
titleSSH to a remote computer
# General form:
ssh <user_name>@<full_host_name>

# For example
ssh abattenh@ls6.tacc.utexas.edu

...

Code Block
languagebash
titleFor loop to count sequences in multiple FASTQs
for fname in *.gz; do
   echo "$fname has $((`zcat $fname | wc -l` / 4)) sequences"
done

quotes matter

We saw how double quotes allow the shell to evaluate certain metacharacters in the quoted text.

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