Page Comparison

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:
  • Windows 10+
    • Command Prompt and PowerShell programs have ssh and scp (may require latest Windows updates)
      • Start menu → Search for Command
    • Putty – http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
      
      • simple Terminal and file copy programs
      • download either the Putty installer or just putty.exe (Terminal) and pscp.exe (secure copy client)
    • Windows Subsystem for Linux – Windows 10 Professional includes a Ubuntu-like bash shells
      • See https://docs.microsoft.com/en-us/windows/wsl/install-win10
      • We recommend the Ubuntu Linux distribution, but any Linux distribution will have an SSH client

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

# General form:
ssh <user_name>@<full_host_name>

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

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Of course Google works on 3rd party tools also (e.g. search for bwa manual)

Terminal input

Literal characters and metacharacters

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# You mis-type thea command name, ofor a command that is not installed on your system
ls6:~$ lzcatt
catt: command Command 'lz' not found,
but
can# beYou installedtry with:to aptuse installan mtoolsunsupported Pleaseoption
askls6:~$ yourls administrator.-z
ls: #invalid Youoption enter something that is close to an existing, or known, command
ls6:~$ catt
Command 'catt' not found, did you mean:
  command 'cat' from deb coreutils (8.30-3ubuntu2)
  command 'catty' from deb node-catty (0.0.8-1)
  command 'ratt' from deb ratt (0.0~git20180127.c44413c-2)
Try: apt install <deb name>

# You try to use an unsupported option
-- 'z'
Try 'ls --help' for more information.

# You specify the name of a file that does not exist
ls6:~$ ls -zxxx
ls: invalid option --cannot access 'zxxx': TryNo 'ls --help' for more information.such file or directory

# You specifytry theto name ofaccess a file that does not exist or directory you don't have permissions for
ls6:~$ ls xxx
ls: cannot access 'xxx': No such file or directorycat /etc/sudoers
cat: /etc/sudoers: Permission denied

Getting around in the shell

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• single Tab – completes file or directory name up to any ambiguous part
  • if nothing shows up, there is no unambiguous match
• Tab twice – display all possible completions
  
  • you then decide where to go next
• shell completion works for commands too (like python bowtie)

Absolute and relative pathname syntax

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