From e077d60ab634fdeee87be6c9015d3ed21d422714 Mon Sep 17 00:00:00 2001
From: Fanny Wegner <fwegner@imm.uzh.ch>
Date: Fri, 24 Feb 2023 15:11:49 +0100
Subject: [PATCH] Update 3 files
- /exercises/UNIX_HPC_cheat_sheet.md
- /exercises/UNIX_HPC_exercise_instructions.md
- /README.md
---
README.md | 5 +-
exercises/UNIX_HPC_cheat_sheet.md | 40 ++++-
exercises/UNIX_HPC_exercise_instructions.md | 159 +++++++++++++++++++-
3 files changed, 201 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index fcc5fe1..bb60ef4 100644
--- a/README.md
+++ b/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)
diff --git a/exercises/UNIX_HPC_cheat_sheet.md b/exercises/UNIX_HPC_cheat_sheet.md
index 8911646..6a25e03 100644
--- a/exercises/UNIX_HPC_cheat_sheet.md
+++ b/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
```
diff --git a/exercises/UNIX_HPC_exercise_instructions.md b/exercises/UNIX_HPC_exercise_instructions.md
index 436d070..c6d0c7b 100644
--- a/exercises/UNIX_HPC_exercise_instructions.md
+++ b/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>
+
+
+
--
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