---+ 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%
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Topic revision: r7 - 2024-07-09 - JeffreyBarrick