Update 3 files

- /exercises/UNIX_HPC_cheat_sheet.md
- /exercises/UNIX_HPC_exercise_instructions.md
- /README.md

README.md

@@ -4,12 +4,15 @@ Welcome to the home page of the Microbial Bioinformatics course.
 
 ## Course material
 
-## Introduction to UNIX and HPC
+
+### Introduction to UNIX and HPC
 - [ ] [Introduction to UNIX slides](slides/introduction_UNIX_HPC.pdf)
 - [ ] [Exercise instructions](exercises/UNIX_HPC_exercise_instructions.md)
 - [ ] [Cheat sheet](exercises/UNIX_HPC_cheat_sheet.md)
 
 
+### Assembly
+- [ ] [Exercise instructions](exercises/assembly_exercise_instructions.md)
 
 
 

exercises/UNIX_HPC_cheat_sheet.md

@@ -27,6 +27,7 @@ cp foo.txt bar.txt                                # Copy file
 mv foo.txt bar.txt                                # Move/Rename file
 rm foo.txt                                        # Delete foo.txt
 rm *                                              # Delete all files in current directory 
+ln -s foo bar                                     # Create a link 'bar' to the file 'foo'
 ```
 
 ## Read and manipulate files
@@ -39,6 +40,7 @@ tail foo.txt           # Print bottom 10 lines of file
 nano foo.txt           # Simple file editor
 vi foo.txt             # Advanced file editor 
 wc foo.txt             # List number of lines words and characters in the file
+cut -d [delimiter] -f [field] foo.txt     # Cuts out the specified fields that are separated by the specified delimiter     
 ```
 
 ## Input and Output
@@ -47,7 +49,43 @@ wc foo.txt             # List number of lines words and characters in the file
 echo "Hello world!"         # Print statement to standard output
 echo "foo" > bar.txt        # Direct output into file. Overwrites file if it already exists.
 echo "foo" >> bar.txt       # Direct output into file and append if it already exists. 
-command 1 | command2        # Directs output from command1 as standard input into command2    
+command1 | command2         # Directs output from command1 as standard input into command2    
+```
+<br><br>
+
+
+
+# SLURM Cheat Sheet
+
+## Connect to Science Cluster
+
+```bash
+ssh shirtname@cluster.s3it.uzh.ch
+```
+
+
+## Submitting jobs
+
+In a script `myjob.sh`:
+```bash
+#!/usr/bin/env bash
+#SBATCH --cpus-per-task=[number]
+#SBATCH --mem=[memory]
+#SBATCH --time=[hr:min:sec]
+#SBATCH --job-name=[name]
+#SBATCH --output=[name]_%j.out
+#SBATCH --error=[name]_%j.err
+
+# load any required modules 
+module load [module name]
+
+command1
+command2
+command3
+```
+Submit script as job to the computing nodes:
+```bash
+sbatch myjob.sh
 ```
 
 

exercises/UNIX_HPC_exercise_instructions.md

@@ -90,4 +90,161 @@ the content of directories.
 
 </p>
 </details>
-<br>
\ No newline at end of file
+<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>
+
+
+