(r7) Barrick Lab :: ProtocolsUnixCommandsQuickReference

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

---++ Disk Space
The =du= command is verbose and confusing if you run it without options. Here is how to get a human-readable output and a grand total for the path argument (omit for current directory).

%CODE{bash}%
du -hc
%ENDCODE%

---++ 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%

---++ Useful Unix Commands

%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}%
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>

---++ Adding Directories to the PATH Variable

When you invoke commands such as <code>python3</code> via at the command line, your shell searches all file directories listed in your =$PATH= in order to execute that command. Errors such as "command not found" when you try to run a program mean you need to add the directory containing that program to your PATH. <p>

To show the current directories that are in your =$PATH= use this:
%CODE{bash}%
echo $PATH</code> 
%ENDCODE%

To add a directory to your =$PATH= you can run this command
%CODE{bash}%
PATH=/your/directory/here:$PATH</code>
%ENDCODE%

%COLOR{red}%Be sure that you include the colon and the =$PATH= part of this. If you leave them off then your shell will not know where to look for built-in commands like =ls=, =cd=, etc.!%ENDCOLOR%

Generally, you want to add the given directory to the end or the beginning of your PATH variable list, since when you invoke a command, the directories will be searched from beginning to end and the first match will be the one that is run. Because this can lead to confusion, there is even a command you can use that gives you the path to the executable that will be run if you type a command:

%CODE{bash}%
which <command>
%ENDCODE%
Barrick Lab > ComputationList > ProtocolsUnixCommandsQuickReference
Contributors to this topic
JeffreyBarrick, LucyLeblanc
Topic revision: r7 - 2024-07-09 - 21:31:17 - Main.JeffreyBarrick