Unix Command Cheat Sheet
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.bash_profile, .profile files
A startup script that gets executed every time a session is started interactively. You can put any command in that file that you could type at the command prompt. Put commands here to set up your particular environment, and to customize things to your preferences (such as paths, aliases, modules to load).
File Editors
- Linux text editors installed at TACC (nano, vi, emacs). These run in your terminal window. vi and emacs are extremely powerful but also quite complex, so nano may be the best choice as a first local text editor.
- Text editors or IDEs that run on your local computer but have an SFTP (secure FTP) interface that lets you connect to a remote computer (Notepad++ or Komodo Edit). Once you connect to the remote host, you can navigate its directory structure and edit files. When you open a file, its contents are brought over the network into the text editor's edit window, then saved back when you save the file.
- Software that will allow you to mount your home directory on TACC as if it were a normal disk e.g. MacFuse/MacFusion for Mac, or ExpanDrive for Windows or Mac ($$, but free trial). Then, you can use any text editor to open files and copy them to your computer with the usual drag-drop.
As we will be using nano throughout the class, it is a good idea to review some of the basics. nano is a very simple editor available on most Linux systems. If you are able to use ssh, you can use nano. To invoke it, just type:
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nano (or)
nano <filename>
You'll see a short menu of operations at the bottom of the terminal window. The most important are:
- ctl-o - write out the file
- ctl-x - exit nano
You can just type in text, and navigate around using arrow keys. A couple of other navigation shortcuts: - ctl-a - go to start of line
- ctl-e - go to end of line
Be careful with long lines – sometimes nano will split long lines into more than one line, which can cause problems in our commands files.
Naming Files
Try to find a convention and stick to it when naming files and directories. But, most importantly:
- Case matters: directory named BioITeam is different from directory named bioiteam.
- Do not use white spaces in file names: Though you may be tempted to name your directory directory my raw data, such naming makes sense when you are looking at the directory visually on your mac finder or windows explorer, but in command line, space means next option. So, mkdir my raw data will actually make 3 directories: my, raw, and data. Use uppercase, or underscores instead of white spaces like like my_raw_data.
- Be careful with using special characters : Typically, underscores,dashes, periods are ok in filenames. But avoid, punctuations and other such special characters. A directory called called sarah's raw data data would be a bad idea.
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