Basic Linux Intro
From Genome Analysis Wiki
(Redirected from Basic Unix/Linux Intro)
Unix/Linux Basic Commands
Use man to see the options for each command (especially grep)
| Get more details on a given command | man command |
| Change Directories | |
| Move to a different Directory | cd pathToGoTo |
| Move up a directory | cd .. |
| Move up 2 directories | cd ../.. |
| See what directory you are in | pwd |
| Look in Directories | |
| See what files are in the current directory | ls |
| See what files are in a different directory | ls pathToDir |
| See hidden files (start with .) | ls -a |
| See detailed file listing | ls -l |
| Copy/Move/Link Files | |
| Copy a file | cp origFile newFileName |
| Copy a file to current directory with original name | cp origFile . |
| Move a file | mv origFile newFileName |
| Link to a file (rather than copy - uses less space/quicker it is not a new file, just a reference to the original. If you change the linked file, you change the original) | ln -s origFile newFile |
| Remove Files/Dirs & Create Dirs | |
| Remove/Delete a file | rm fileName |
| Create a new directory | mkdir dirName |
| Create a directory & subdirectories | mkdir -p dirName/subDir/subDir2 |
| Remove a directory | rmdir dirName |
| Search | |
| Search for a file in dir/subdirs (use * for wildcard matching) | find . --name "fileName" |
| Search for text in files (can use * for all files) | grep textToFind filesToSearch |
| Look at Files | |
| Look at file | less fileName -or- more fileName |
| Look at just beginning of the file | head fileName |
| Look at end of file | tail fileName |
| Compare files | diff file1 file2 |
| Permissions | |
| Change directory/file permissions | chmod newPermissions fileName |
| Processes | |
| See what you have running | ps -ef | grep yourUserName |
| Kill/end a job you don't want running | kill -9 process#FromPs |
Notes on directories:
- . Refers to current directory
- .. Refers to one directory up
- ../.. refers to 2 directories up
- ../../.. refers to 3 directories up
- (etc)
The '*' star character is used to match any characters (0 or more). You can use it anytime you need to specify a filename(s) and it will use all the files in the current directory/path. It can also be used to wildcard match a partial file name: filePrefix* will match filePrefix1.txt and filePrefix2.txt
You can use alias to setup an alias for a command. See man to see how it is used.
Additional Resources
For more information, see:
CSG Documentation [AWK, BASH, UNIX commands and etc.]
