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Just Geomorphology

Intro to the shell

  • A very short intro on the Linux terminal here.
  • A longer intro on the Linux terminal here.

Basic shell commands

Command Use
pwd Print current (working directory)
ls my_directory List files in a directory
cd my_path Define (go to) current directory
cd Return to HOME directory
cd ../ Go to parent directory
rm my_file Remove file (!no way back!)
mkdir my_directory Create directory
rmdir -rf my_directory Remove directory (!no way back!)
cp path_to_source path_to_destination Copy file or directory
mv path_to_source path_to_destination Move file or directory
Ctrl-Shift-C Copy some text in vim editor
Ctrl-Shift-V Paste some text in vim editor
vim path_to_text_file Open text file using vim
unzip path_to_archive_file -d path_to_destination Unzip a .zip archive in a directory
Ctrl-C Cancel current command

Good practices

Working on the terminal can difficult in the beginning. One difficulty is to always know where you are located in the file tree.

  • Use pwd command to print the current directory.

  • Use ls (list) or ll (long list) commands to print the content of the current directory. Use it often… Typically after a command that create outputs, to check whether they are created…

    ls-command

  • Use Tab key to auto-complete file names and directory names. Hit Tab key again to get a list of possibilities, if there are several ones.
  • Use Up and Down arrows of the keyboard to navigate in the history of commands that you already executed.

Paths (examples on the Pelican server)

Some facts about paths to directories and files:

  • When you connect to the Pelican server, you land in your HOME directory.
  • The absolute path of your HOME directory is: /home/elic/MY_LOGIN.
  • Anywhere in the file tree, execute the cd command to return the HOME directory.
  • Absolute paths are always written with respect to the root of the file tree, i.e. /.
  • A typical absolute path to the DEM file would be: /home/elic/MY_LOGIN/lsdtt/data/dem-analysis/mnt-ambleve-10m.tif. Notice the / at the beginning of the path, indicating that it is an absolute path, i.e. starting from the root.
  • A typical relative path to the DEM file, if you are located in your HOME directory: lsdtt/data/dem-analysis/mnt-ambleve-10m.tif. Note that there is no / at the beginning of the path.
  • Relative paths are always expressed relatively to the current directory.
  • To know the current directory, use the pwd command (print working directory).

Sequence of example commands

Type and execute the following sequence of commands to learn how to communicate with the server:

# Print working directory
pwd
# List files in current directory
ls
# create new directory
mkdir dem-analysis
# create file in dem-analysis directory
vim dem-analysis/params.txt
# type i to activate insert mode, write something, hit Esc to quit edit mode, type ":wq" to write and quit the file
# List files in dem-analysis directory
ls dem-analysis
# Enter dem-analysis directory
cd dem-analysis
# List files in current direct
ls
# List files in parent directory
ls ../
# Create new directory in current directory
mkdir outputs
# list files in current directory
ls
# Copy params.txt into outputs directory with a new name
cp params.txt outputs/params-v2.txt
# Return to HOME directory
cd
# Enter outputs directory
cd dem-analysis/outputs
# Modify params-v2.txt file. Use "Ctrl-Shift-C" to copy and "Ctrl-Shift-V" to paste text.
vim params-v2.txt
# Print working directory
pwd
# Return to dem-analysis directory. The ~ is a way to create a path from the HOME directory. Useful when your are "lost" in the file structure.
cd ~/dem-analysis
# Copy outputs as a new directory. The "-r" parameter is for "recursive", i.e. it will copy all subdirectories too.
cp -r outputs outputs-v2
# List files in current directory
ls
# Delete outputs/params.txt
rm outputs/params-v2.txt
# Delete params.txt in current directory. The "-f" parameter is for "force".  
rm -f params.txt
# Delete outputs-v2.
rm outputs-v2
# To delete non-empty directories, do not forget the "-rf" parameters
rm -rf outputs-v2
# List files in current directory
ls
# Return to HOME directory
cd
# Delete dem-analysis directory
rm -rf dem-analysis