I was mostly unfamiliar with using a terminal before I started my PhD. After ten years, I’m still unfamiliar with using a terminal, though I’m probably not as bad as most. This page deals with how to install commonly used structural biology software on a fresh, Ubuntu install. Below is a table detailing common Linux commands and how to use them. I’ll probably add more here as time goes on.
| Command | Action | Flags | Examples | Notes |
|---|---|---|---|---|
| ls | list | -l (long), | Lists all items in a directory | |
| ll | long list | -a (all), | Same as ls -l. Lists all items in a directory as well as attributes. | |
| mkdir | make a directory | mkdir newdirectory | Will make a new directory in current location | |
| pwd | present working directory | To find out your current location | ||
| echo | write specified file to text | echo “this is a text file” > testfile.txt | This will write the text in quotation marks into a textfile.txt | |
| mv | move | mv *.tiff ./Movies | Moves all files with a .tiff extension to a directory /Movies | |
| du | disk usage | -h (human readable) | du -h | Displays disk use of the directory in a human readable format |
| ls | wc -l | List number of files | [username@glogin2 frames]$ ls | |
| 15194 | Lists the number of files in a directory. Useful for checking to see if the number of micrographs extracted or moved matches the number in a collection | |||
| sar -u | CPU usage in terminal | 5 | sar -u 5 | Lists CPU use in the terminal, the flag indicates every 5 seconds it will update |
| pkill <program> | Kills a program | pkill google-chrome | Will kill a particular application from command line | |
| module <flag> | lists software modules | avail | ||
| list | ||||
| load | ||||
| purge | ||||
| unload | module avail | |||
| module list | ||||
| module load conda/23.1.0 | ||||
| module purge | ||||
| module unload relion | Module avail: Lists available modules | |||
| Module list: Lists loaded modules | ||||
| Module load: Loads selected module | ||||
| Module purge: unloads all modules | ||||
| Module unload: unloads selected module | ||||