Shells

We use the bash linux shell exclusively for the interactive command line and shell scripting. In general, this is the most powerful shell and the professional's choice.

Setup scripts

• ~/.bash_profile is executed once when you login.
  • When you first get a mu2e account, we recommend that you copy the Mu2e example .bash_profile from: ExampleBashProfile
  • It sources /cvmfs/fermilab.opensciencegrid.org/products/common/etc/setups.sh, which initializes the UPS system for use in your shell. For details of how the UPS system is used see here .
  • The recommended practice is that you not modify this file. Instead create a file named ~/.my_bash_profile and put your personal customizations there. The reason is that it will be easier for you if we later change the recommended ~/.bash_profile.
• ~/.bashrc is executed for interactive non-login shells
  • When you first get a mu2e account, you will be given an example which would usually be modified
  • set the prompt
  • set any aliases
  • a good style is to leave the example untouched except to source a separate file (such as ~/.mybashrc) with your customizations. This always makes it clear what you are adding.
• we do not use ".login" or ".profile" which are variants for .bash_profile
• we do not recommend setting up UPS packages in the bash login scripts since this can get confusing
• the lab systems will also usually execute /etc/profile.d/*.sh and /etc/bashrc

Standards

• scripts that intended to be executed by the average user at the command line, should be added to the user's path and can be named with no extension, so it looks built-in.
• scripts that are used in complex packages, or for special purposes, such as in monitoring, should have extension ".sh"
• scripts intended to be sourced should have the extension ".sh".

References

The Linux Documentation Project publishes a number of guides that are available online. We suggest:

• Bash Guide for Beginners, a comprehensive introduction.
• BASH Programming - Introduction HOW-TO, a shorter but less complete introduction.
• Advanced Bash Scripting Guide, starts at the beginning put goes more quickly to advanced ideas.

Beginner Cheat Sheet

Files and directories

cp <x> <y> 	% copy <x> to <y>
mv <x> <y>	% move <x> to <y>
mkdir <x> 	% makes new directory <x>
pwd 		%shows current directory
cd <x>		% goes into folder <x>
rm <x> 		% remove file <x>
ln -s <x> <y>	% makes a soft link between real file <x> and local pointer <y>
ls 		% lists documents in current directory
cat <file> 	% list the whole file
more <file> 	% types <file> in chunks, <space> goes to next chunk
less <file>	% similar to more
head <file> 	% types the first N lines
tail <file>	% types the last N lines
find *		% list all of the files

Process management

CTL-Z	% pause the current process and return to console
bg 	% allow the process you just paused to run in background
jobs 	% shows what you're running
ps 	% shows processes 

<c> > file	% output of command c goes to file <file>
<c> >& file	% errors from command c goes to file <file>
<c> >> file	% appends output of <c> onto end of <file>
<c> >>& file	% appends error of <c> onto end of <file>

Help

man <c>	% help on command <c>
<c> -h	% sometimes has help this way as well

Editing and strings

sed s/<a>/<b>/ <file> > 
grep <a> <b>	% print out all lines in  <b> which contain string <a>
sort <a>	% sort the file a
diff <a> <b>	% print out the difference between <a> and <b>
xemacs <a>	% edit the file <a>

Environmentals

export <X>=<y> 		% will make $X refer to <y>
export PATH=<y>:${PATH} 	%will append <y> to $PATH

important environmentals are:

$HOST     % this computers's name
$USER    % your username
$HOME 		% your home area
$PWD 	            	% the current directory
$PATH 	            	% where unix looks for code to execute
$PYTHONPATH 	% where unix looks for python modules to import
$LD_LIBRARY_PATH	% where unix looks for shared libraries

You normally want to append to the PATH. Just setting them to <x> wipes out all the other stuff they were already set to.