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Documentation pages:
Useful keys in the Terminal
| , "pipe" connects output of one command to another (see example 'grep' below)
~ , "tilde" stands for "home" directory
tab , "tab" autocompletion of paths and commands in the terminal. Extremely useful to check if the command is actually valid.
ctrl + c , not "copy", it actually kills a process in the terminal.If you want to copy use middle mouse or mousepad-specific features.
ctrl + Z , then bg puts a running process in the terminal into the background , same as starting a process with &. Example: relion &
Some useful commands in the Terminal:
- listing the content of the current working directory:
$ ls -lrt - changing directory:
$ cd /path/to/dir - creating a directory:
mkdir /path/to/dir - removing a directory:
rm -r /path/to/dir - copying a directory or file:
cp -r (-r only for folders) /path/to/file /destination/of/file - editing files:
emacs <name-of-file>ornedit <name-of-file>orvim (advanced) - showing file contents in the terminal:
more <name-of-file> - showing the size of folders/files in one specific folder:
du –max-depth 1 -h - searching for a specific pattern in a file:
more <name-of-file> | grep 'pattern'
~/.bashrc file
- The ~/.bashrc file is similar to a "config" file that is executed every time that you open a new terminal.
- Inside the ~/.bashrc file, paths, variables and user-specific settings can be edited (use any editor), after changing, the terminal needs to be closed and reopened in order to make changes available.
- Examples that change the bashrc file: conda installations, cryosparc etc..
Software
Installations
Software can be used in two ways:
- load the available software via a Pmodule
- Install your software locally (in
/data/user/$username)
To check, which executable you are actually running on and which version is running, you can do: $ which python or $ python --version.