ProtocolsUnixCommandsQuickReference < Lab

---+ Unix Commands Quick Reference
Useful commands and flags that we get tired of looking up...

---++ Alphabetical Reference

%CODE{bash}%
cat yourfile.txt
%ENDCODE%
Prints the contents of the given file to the console.

%CODE{bash}%
cd put/target/directory/here
%ENDCODE%
Changes the working directory to whatever path is typed after cd. Without an additional argument, cd brings one back to the home directory.

%CODE{bash}%
du -hc 
%ENDCODE%
Get a human-readable output of disk space usage. If you add =*= then it will give you this for all files in the current directory.

%CODE{bash}%
fgrep "words" yourfile.txt
%ENDCODE%
Print only lines in a file containing the given "words" in a particular file.

%CODE{bash}%
find word*
%ENDCODE%
Locates and gives file names of all files in the working directory containing word in the beginning of the file name. The * represents a wildcard so it can be placed before, after, or both in order to find files that contain the given query in a particular part of the file name.<p>

%CODE{bash}%
kill process
%ENDCODE% Ends a particular process. Note that you can type =killall= to end multiple processes that match the name that is input.

%CODE{bash}%
ls
%ENDCODE%
Lists the contents of the working directory. Add =-a= to include invisible files. Add =-l= to show more information about each file such as its owner and permission flags.

%CODE{bash}%
mkdir directoryname
%ENDCODE%
Makes a directory with a name specified by the user.

%CODE{bash}%
nl yourfile.txt
%ENDCODE%
Numbers all the lines of a file.

%CODE{bash}%
ps
%ENDCODE%
Lists all process currently running.

%CODE{bash}%
pwd
%ENDCODE%
Prints the working directory path to the console.

%CODE{bash}%
rm yourfile.txt
%ENDCODE%
Deletes a given file.

%CODE{bash}%
rmdir yourdirectory
%ENDCODE%
Deletes a given directory.

%CODE{bash}%
source yourfile
%ENDCODE%
Reads and executes commands from the given file in the current environment.

%CODE{bash}%
which yourprogram
%ENDCODE%
Prints the the full path of the program to the console (note that its directory must be in your =$PATH=). Adding an =-a= after which prints all instances of the program.<p>

---++ Fixing Line Endings

If you get odd errors after transferring a text file from a PC or Mac to a Unix machine, it's likely that you have a problem with [[http://en.wikipedia.org/wiki/Newline][newline characters]]. This is especially common when editing files in Excel and saving them to tab-delimited or comma-delimited files for input into. You can generally avoid this problem and fix the line endings by using an industrial strength text editor. This command converts Mac line endings in a saved Excel file to Unix line endings.

%CODE{bash}%
tr "\r" "\n" < input.tab >.converted.tab
%ENDCODE%

---++ Merging commands to be serial on TACC

Sometimes you have 96 short jobs that you want to run serially 8 at a time on 12 cores rather than requesting 96 cores. This command will combine every 8 lines in a file into one line separated by && so that these commands are now run on one core.

%CODE{bash}%
paste -s -d'#######\n' commands | sed "s/#/ \&\& /g" > commands8
%ENDCODE%

---++ Adding your path to the command prompt

Add to your =.bashrc=, =.zshrc=, or similar shell startup script:
%CODE{bash}%
export PS1='\w\$ '
%ENDCODE%
Now your current working directory will show up as part of your prompt. This can save you a lot of time typing =ls=.
Barrick Lab > ComputationList > ProtocolsUnixCommandsQuickReference
Topic revision: r8 - 2024-07-09 - 22:32:58 - Main.JeffreyBarrick