Linux tutorial in docs

config/others/linux-tutorial.yml

@@ -1,6 +1,7 @@
 site_name: Linux tutorial
 docs_dir: docs/linux-tutorial
 nav:
+  - Introduction: index.md
   - Getting Started: getting_started.md
   - Navigating: navigating.md
   - Manipulating files and directories: manipulating_files_and_directories.md

config/templates/hpc.template

@@ -32,7 +32,15 @@ nav:
 {%- if site == 'Gent' %}
       - GPU clusters: gpu.md
       - Cron scripts: crontab.md
-      - Linux tutorial: only/gent/linux-tutorial/getting_started.md
+  - Linux tutorial:
+    - Introduction: only/gent/linux-tutorial/index.md
+    - Getting Started: only/gent/linux-tutorial/getting_started.md
+    - Navigating: only/gent/linux-tutorial/navigating.md
+    - Manipulating files and directories: only/gent/linux-tutorial/manipulating_files_and_directories.md
+    - Uploading files: only/gent/linux-tutorial/uploading_files.md
+    - Beyond the basics: only/gent/linux-tutorial/beyond_the_basics.md 
+    - Common pitfalls: only/gent/linux-tutorial/common_pitfalls.md
+    - More on the HPC infrastructure: only/gent/linux-tutorial/hpc_infrastructure.md
 {%- endif %}
   - Software-specific Best Practices:
       - Apptainer/Singularity: apptainer.md

mkdocs/docs/HPC/only/gent/linux-tutorial/common_pitfalls.md

@@ -1,5 +1,8 @@
 # Common Pitfalls
-## Files
+
+This page highlights common pitfalls in Linux usage, offering insights into potential challenges users might face. 
+By understanding these pitfalls, you can avoid unnecessary hurdles.
+
 ### Location
 
 If you receive an error message which contains something like the
@@ -125,8 +128,7 @@ smallest of problems!**
     examples. There is an associated book which gets a lot of good
     reviews
 
-3.  [The Linux Documentation Project](http://www.tldp.org/guides.html) -
-    More guides on various topics relating to the Linux command line
+3.  [The Linux Documentation Project](http://www.tldp.org/guides.html): More guides on various topics relating to the Linux command line
 
 4.  [basic shell
     usage](http://linuxcommand.org/lc3_learning_the_shell.php)
@@ -136,6 +138,4 @@ smallest of problems!**
 
 6.  [MOOC](https://www.edx.org/course/introduction-linux-linuxfoundationx-lfs101x-0)
 
-# Q & A
-
 Please don't hesitate to contact in case of questions or problems.

mkdocs/docs/HPC/only/gent/linux-tutorial/getting_started.md

@@ -220,3 +220,5 @@ Exercises
     newline
 
 -   How do you get help on using the `man` command?
+
+Next [chapter](navigating.md) teaches you on how to navigate.

mkdocs/docs/HPC/only/gent/linux-tutorial/index.md

@@ -0,0 +1,24 @@
+# Introduction
+
+Welcome to the Linux tutorial, a comprehensive guide designed to give you essential skills for smooth interaction within a Linux environment.
+
+These skills are important to the {{ hpcinfra }}, which operates on {{ operatingsystembase }}.
+For more information see [introduction to HPC](https://docs.hpc.ugent.be/introduction).
+
+The guide aims to make you familiar with the Linux command line environment quickly.
+
+The tutorial goes though the following steps:
+
+1. [Getting Started](getting_started.md)
+2. [Navigating](navigating.md)
+3. [Manipulating files and directories](manipulating_files_and_directories.md)
+4. [Uploading files](uploading_files.md)
+5. [Beyond the basics](beyond_the_basics.md)
+
+Do not forget [Common pitfalls](common_pitfalls.md), as this can save you some troubleshooting.
+
+### Useful topics
+
+- [More on the HPC infrastructure](hpc_infrastructure.md).
+- [Cron Scripts](https://docs.hpc.ugent.be/crontab): run scripts automatically at periodically fixed times, dates, or intervals.
+

mkdocs/docs/HPC/only/gent/linux-tutorial/manipulating_files_and_directories.md

@@ -273,3 +273,5 @@ you remember:
 
 8.  gzip `hostname.txt`, see how much smaller it becomes, then unzip it
     again.
+
+The next [chapter](uploading_files.md) is on uploading files, especially important when using HPC-infrastructure.

mkdocs/docs/HPC/only/gent/linux-tutorial/navigating.md

@@ -1,6 +1,9 @@
 Navigating
 ==========
 
+This chapter serves as a guide to navigating within a Linux shell, giving users essential techniques to traverse directories. 
+A very important skill. 
+
 Current directory: "pwd" and "\$PWD"
 ------------------------------------
 
@@ -203,3 +206,5 @@ Exercises
 
 -   See how home directories are organised. Can you access the home
     directory of other users?
+
+The [next](manipulating_files_and_directories.md) chapter will teach you how to interact with files and directories.

mkdocs/docs/HPC/only/gent/linux-tutorial/uploading_files.md

@@ -111,3 +111,5 @@ information about rsync.
 2.  Upload a file to a subdirectory of your personal `$VSC_DATA` space.
 
 3.  Create a file named `hello.txt` and edit it using `nano`.
+
+Now you have a basic understanding, see next [chapter](beyond_the_basics.md) for some more in depth concepts.