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Applied CyberInfrastructure ConceptsISTA 420/520 Fall 2013
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Nirav Merchant ([email protected])Bio Computing & iPlant CollaborativeEric Lyons ([email protected])Plant Sciences & iPlant CollaborativeUniversity of Arizonahttp://goo.gl/p4j3m or https://sites.google.com/site/appliedciconcepts/
Will Computers Crash Genomics? Science Vol 331 Feb 2011
Tasks for todayManaging your VMAdd user, permission, security considerations etc.Understanding where the files areTerminal, editors etcShell and scriptingStart building your “Data Science ToolBox”
Step #1 for Big Data ToolkitCommand line competency
PermissionsWhy do you need them ?What is a ACL (Access Control List) ?The UNIX model of permissions (next slides are
from Greg Wilson at http://software-carpentry.org)
Path statement and finding things
Has unique user name and user ID
user
Has unique user name and user ID
User name is text: "imhotep", "larry", "vlad", …
user
user
Has unique user name and user ID
User name is text: "imhotep", "larry", "vlad", …
User ID is numeric (easier for computer to store)
user group
user group
Has unique group name and group ID
user group
Has unique group name and group ID
User can belongs to zero or more groups
user group
Has unique group name and group ID
User can belongs to zero or more groups
List is usually stored in /etc/group
user group all
user group all
Everyone else
user group all
Has user and group IDs
user group all
read
user group all
read
write
user group all
read
write
execute
user group all
read ✔ ✔ ✗
write ✔ ✗ ✗
execute ✗ ✗ ✗
user group all
read ✔ ✔ ✗
write ✔ ✗ ✗
execute ✗ ✗ ✗
File's owner can read and write it
user group all
read ✔ ✔ ✗
write ✔ ✗ ✗
execute ✗ ✗ ✗
File's owner can read and write it
Others in group can read
user group all
read ✔ ✔ ✗
write ✔ ✗ ✗
execute ✗ ✗ ✗
File's can read and write it
Others in group can read
That's all
Where are my files ?
• Understanding layout of data– Home– Root– Tmp
• Permissions• Storage space and planning for it• Managing runaway items (more in next
class)
Security considerations
• Update your OS (how can you do that ?)• Why you should NEVER run as root
(how do I add a user ?)• Password and keys
(and dual factor)• Ssh foo
What is Shell?
• Shell is– Command Interpreter that turns text that you
type (at the command line) in to actions:– User Interface: take the command from user
• Programming Shell can do– Customization of a Unix session– Scripting– Many Many automation steps
What is Shell?
• Shell is– Command Interpreter that turns text that you
type (at the command line) in to actions:– User Interface: take the command from user
• Programming Shell can do– Customization of a Unix session– Scripting– Many Many automation steps
Customization of a Session
• Each shell supports some customization.– User prompt– Where to find mail– Shortcuts (alias)
• The customization takes place in startup files – Startup files are read by the shell when it
starts up– The Startup files can differ for different shell
Popular Shells
sh Bourne Shell ksh Korn Shell csh,tcsh C Shell (for this course) bash Bourne-Again Shell
Flavors of Unix Shells
• Two main flavors of Unix Shells– Bourne (or Standard Shell): sh, ksh, bash, zsh
• Fast• $ for command prompt
– C shell : csh, tcsh• better for user customization and scripting• %, > for command prompt
• To check shell:– % echo $SHELL (shell is a pre-defined variable)
• To switch shell:– % exec shellname (e.g., % exec bash)
Startup files and why you should care
bash:/etc/profile (out-of-the-box login shell settings) /etc/bash.bashrc (out-of-box non-login settings)/etc/bash.bashrc.local (global non-login settings)~/.bash_profile (login shell user customization)~/.bashrc (non-login shell user customization)
~/.bash_logout (user exits from interactive login shell)
http://cli.learncodethehardway.org/bash_cheat_sheet.pdf
Some Special Keys
• How do you invoke tcsh ?• Ctrl-U = Delete everything on the command-
line• Ctrl-A = Move cursor to the front• Ctrl-E = Move cursor to the end• Ctrl-P = Set the current command-line to the
previous command• Ctrl-N = Set the current command-line to the
next command• TAB = Filename completion
Preview pieces of toolbox
• http://datascienceatthecommandline.com/• We will work though Step 5 and go straight to
commands
Next class
Preparing to play with your data set– Can you download a piece of it ?
Learn about space and process management Introduction to shell scripting and automationStart building your Big Data command line tool
kit
