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-## Before you start
-
-If you have questions about any command, you can always type `man [command]` to get an explanation and all possible additional options.
-
-
-
-## Exercise 1 - Navigating the filesystem on command line
-
-**Objective:** get familiar with navigating the directory tree and listing
-the content of directories.
-
-1. **Print your current working directory** with the `pwd` command. This will
- show you where you currently are in the directory tree.
-
-2. **Navigate to the `exercises/` directory** (the one you unpacked from the
- zip archive file). If you are already in the `exercises/` directory,
- navigate to its parent with `cd ..` and then come back to it.
-
-3. **Try to run the command `cd .`**. What happens? What does the `.` stand
- for?
-
-4. **List the content** of the `exercises/` directory with `ls`, `ls -l`,
- `ls -lh`, and `ls -lha`.
- * What do the `-l`, `-h` and `-a` options do?
- * **Hint:** you can use `man ls` to display the help for the `ls` command.
- To exit the help, simply type `q` on your keyboard.
- * *Note:* one-letter options can be grouped together, so `ls -lha` is the
- same as `ls -l -h -a`.
- * *Note:* some options have both a "short" and a "long" form. E.g. `ls -a`
- is the short form for `ls --all`.
-
-
-<br>
-<details><summary><b>Exercise solution</b></summary>
-<p>
-
-1. Printing the current working directory:
-
- ```sh
- pwd
- ```
-
-2. Navigate to the current directory, or navigate in and out of it.
-
- ```sh
- # If you are not already in the practicals directory.
- # Note: in the command below, you need to replace /path/to/directory/ with
- # the actual absolute or relative path of the directory where your
- # "practicals" directory is located.
- cd /path/to/directory/exercises
- pwd
-
- # If you are already in the practicals directory.
- cd .. # Change to parent directory.
- pwd #
- ls -l #
- cd exercises/ # Go back into the practicals/ directory.
- ```
-
-3. The `.` symbol is a shortcut for the current directory. So running `cd .`
- has no effect since it simply changes to the same directory we are already
- in.
-
- The `.` shortcut is useful in some situations. E.g. if you want to copy
- a file to the current directory you can do `cp /file/to/copy .`, or you
- can run an executable located in the current directory with `./run_me.sh`.
-
-
-4. Listing the content of the `exercises/` directory with different `ls`
- options. the effect of the different options is described in the comments
- of the code block below.
-
- ```sh
- ls # Prints the names of files and directories
- ls -l # List content of the subdirectory in "long listing" format. This
- # provides additional details for each file/directory, such as
- # its permissions, its size and its last modified date.
- ls -lh # Adding the "-h" option displays file sizes in "human readable"
- # format. The size of files are shown in kB, MB, GB, instead of
- # their size in bytes (octets).
- ls -lha # Adding the "-a" option additionally displays hidden files and
- # directories. These are files/directories whose name starts with
- # a dot ".". The "-a" is the
- # Hidden files are often used to store program configurations.
- ```
-
- **Tip:** It is possible to define a shorthand for longer commands that you use often, a so called `alias`. On Science Cluster, there are already some pre-defined useful aliases, among them `ll` (standing for `ls -lFh`) and `la` (standing for `ls -lA`).
-
-
-
-</p>
-</details>
-<br>
-
-## Exercise 2 - Creating and moving directories and files
-
-**Objective:** learn to use the `mkdir`, `cp` and `mv` commands.
-
-1. **Create directories** with the `mkdir` command:
- * At the root of the `exercises/` directory, create 2 new
- sub-directories: `species_by_genus` and `species_by_common_name`.
- * In `exercises/species_by_genus/`, create 2 new sub-directories:
- `Dendrolagus` ([tree-kangaroos](https://en.wikipedia.org/wiki/Tree-kangaroo))
- and
- `Crocidura` ([a genus of shrews](https://en.wikipedia.org/wiki/Crocidura)).
- * In `exercises/species_by_common_name/`, create 2 new sub-directories
- named `B`, and `R`.
-
-2. **Copy files** using the `cp` command:
- * From the directory `RedList_mammals/`, make a copy of all files of the
- genuses `Dendrolagus` and `Crocidura` into their respective
- sub-directories in `species_by_genus/`.
- * From the directory `RedList_mammals/`, copy the file for the
- [Red Wolf](https://en.wikipedia.org/wiki/Red_wolf) *Canis rufus* to the
- directory `species_by_common_name/`.
-
-3. **Move and rename files** with the `mv` command:
- * Enter the `species_by_common_name/` directory.
- * In the directory, move the file `Canis_rufus` into subdirectory `R`.
- * Rename the `Canis_rufus` file you just moved into the subdirectory `R` to
- the common name of the species: `Canis_rufus` -> `Red_wolf`.
-
-4. **Copy and rename files** with the `cp` command:
- * Similarly to what we did for the Red Wolf file, we will now copy and
- rename the file for the
- [Black Rhinoceros](https://en.wikipedia.org/wiki/Black_rhinoceros)
- *Diceros bicornis*, but this time in a single step with the `cp` command.
- * Copy the file `Diceros_bicornis` from its original location (in
- `RedList_mammals`) into `species_by_common_name/B`, while directly
- renaming it to the common name of the species: `Black_rhino`.
-
-5. **Copy, rename and delete directories**:
- * Go back to the root of the `exercises/` directory.
- * Copy the entire directory `species_by_genus/Dendrolagus/` with all its
- content to the root of `exercises/`.
- * Rename the directory to `Tree-kangaroos`.
- * Delete the directory `Tree-kangaroos` and its content **in a safe way**.
-
-
-<details><summary><b>Exercise solution</b></summary>
-<p>
-
-1. Create the `IUCN_species_by_genus` and `IUCN_species_by_common_name`
- directories.
-
- ```sh
- # Option 1: create one directory after the other.
- mkdir species_by_genus
- mkdir species_by_common_name
-
- # Option 2: create both directories with a single command.
- mkdir species_by_genus species_by_common_name
-
- # Option 3: use brace expansion to avoid repeating the common part of
- # the directory names.
- mkdir species_by_{genus,common_name}
- ```
-
- Create sub-directories `Dendrolagus` and `Crocidura`:
-
- ```sh
- # Option 1: create sub-directories from the exercises/ directory.
- mkdir species_by_genus/Dendrolagus species_by_genus/Crocidura
-
- # Option 2: enter the species_by_genus/ directory, then create the
- # sub-directories "Dendrolagus" and "Crocidura".
- cd species_by_genus/
- mkdir Dendrolagus Crocidura
- cd ..
-
- # Option 3: same as option 1, but using brace expansion to avoid repetition.
- mkdir species_by_genus/{Dendrolagus,Crocidura}
- ```
-
- Create sub-directories `R` and `B`:
-
- ```sh
- mkdir species_by_common_name/{R,B}
- ```
-
- *Note:* using the `-p` option of `mkdir`, it is possible to create
- multiple levels of directories in a single command. For example, we could
- create all the directories from this exercise in a single command:
-
- ```sh
- mkdir -p species_by_{genus/{Dendrolagus,Crocidura},common_name/{R,B}}
-
- # Pro-tip: if you want to preview the output of a brace expansion by
- # the shell, you can run the command prefixed with "echo": it will print
- # the command that would be executed to the terminal without running the
- # command.
- echo mkdir -p species_by_{genus/{Dendrolagus,Crocidura},common_name/{R,B}}
- ```
-
-2. Copy files for `Dendrolagus` and `Crocidura`:
-
- ```sh
- cp RedList_mammals/Dendrolagus_* species_by_genus/Dendrolagus/
- cp RedList_mammals/Crocidura_* species_by_genus/Crocidura/
- ```
-
- Copy the file for the Red Wolf:
-
- ```sh
- cp RedList_mammals/Canis_rufus species_by_common_name/
- ```
-
-3. Move and rename the Red Wolf file:
-
- ```sh
- cd species_by_common_name/
- mv Canis_rufus R/ # Move the file into its subdirectory.
- mv R/Canis_rufus R/Red_wolf # Rename the files to the common name of the species.
- ```
-
-4. Copy and rename the file for teh Black Rhino in a single `cp` command:
-
- ```sh
- # Note: this assumes you are currently in directory "species_by_common_name".
- cp ../RedList_mammals/Diceros_bicornis B/Black_rhino
- ```
-
-5. Copy, rename and delete a directory:
-
- ```sh
- cd .. # Go back to the root of the `exercises/` directory.
- cp -r species_by_genus/Dendrolagus/ . # Copy the directory and its content.
- mv Dendrolagus/ Tree-kangaroos # Rename the directory.
- ls -l
-
- # To delete the directory in a safe way, we first delete all the files
- # inside it, and then delete the empty directory with "rmdir".
- # Note that "rmdir" will not delete a directory if it's not empty - this
- # is a safety behavior to avoid deleting large number of files by mistake.
- rm Tree-kangaroos/*
- rmdir Tree-kangaroos
- ```
-
- *Note:* the faster way to delete the directory and all of its content would
- be to use the command: `rm -rf Tree-kangaroos`.
-
- This recursively delete the directory, and therefore one has to be careful
- to be deleting the correct directory, as you can otherwise very quickly
- delete large amounts of data by mistake.
-
-</p>
-</details>
-
-
-