Use modules from 'Intro to UPPMAX Day 1'

docs/modules.md

@@ -0,0 +1,281 @@
+# The module system
+
+!!!- info "Learning objectives"
+
+    - Practice using the UPPMAX documentation
+    - Can find pre-installed software from the documentation
+    - Can find pre-installed databases from the documentation
+    - Understand why there is a module system
+    - Can find pre-installed software using the module system
+    - Can load a module
+    - Practice loading the `bioinfo-tools` module first
+
+???- question "For teachers"
+
+    Teaching goals are:
+
+    - Learners have practiced using the UPPMAX documentation
+    - Learners have found pre-installed software from the documentation
+    - Learners have found pre-installed databases from the documentation
+    - Learners understand why there is a module system
+    - Learners can find pre-installed software using the module system
+    - Learners can load a module
+    - Learners can unload a module
+    - Learners understand to load the `bioinfo-tools` module first
+
+    Lesson plan:
+
+    ```mermaid
+    gantt
+      title Modules
+      dateFormat X
+      axisFormat %s
+      section First hour
+      Prior : prior, 0, 5s
+      Present: present, after prior, 2s
+      %% It took me 9 mins, here I do that time x2
+      Challenge: crit, challenge, after present, 18s
+      %% Here I use the same time it took me to give feedback
+      Feedback: feedback, after challenge, 9s
+    ```
+
+    Prior questions:
+
+    - What would happen if all users would be allowed
+      to install software on Rackham?
+    - Describe a situation when two users that have admin rights
+      on the same account of the same computer cannot both be happy
+    - How can one run different versions of the same software
+      on a same computer?
+    - How can we have users use different versions of the same software?
+    - What is the UPPMAX software module system?
+    - What is a module?
+    - Has anyone already used the UPPMAX module system?
+
+## Why?
+
+The module system allows you to run your software,
+of your favorite version, installed by us :-)
+
+Additionally, there are big databases (think terabytes!)
+that are also available to you.
+
+In this session, we'll search for pre-installed software,
+pre-installed databases and use these.
+
+## The `bioinfo-tools` module
+
+The most important module for bioinformaticians is the `bioinfo-tools`
+module. It is loaded as such:
+
+
+```bash
+module load bioinfo-tools
+```
+
+Only after loading it will some other tools appear.
+
+## Exercises
+
+???- question "Need a video?"
+
+    [Here](https://youtu.be/ZuLMoZkGsZk) is a video that shows
+    the solution of these exercises
+
+### Exercise 1: find the software
+
+Go to the UPPMAX documentation at
+[https://docs.uppmax.uu.se](https://docs.uppmax.uu.se),
+then answer these questions:
+
+- Find to list of installed software.
+  Estimate how many pieces of software are installed on Rackham
+
+???- question "Answer"
+
+    One can find the answer at <https://docs.uppmax.uu.se/software/software-table/>,
+    where one can find around 800 pieces of software installed
+
+### Exercise 2: find the databases
+
+Go to the UPPMAX documentation at
+[https://docs.uppmax.uu.se](https://docs.uppmax.uu.se),
+then answer these questions:
+
+- Find to list of databases.
+  Estimate how many collections of databases are installed on Rackham
+
+???- question "Answer"
+
+    One can find the answer at <http://docs.uppmax.uu.se/databases/overview/>,
+    where one can find around 7 collections of databases installed.
+
+### Exercise 3: work with modules
+
+Go to the UPPMAX documentation at
+[https://docs.uppmax.uu.se](https://docs.uppmax.uu.se),
+then answer these questions:
+
+- Find the UPPMAX documentation on modules
+
+???- question "Answer"
+
+    One can find the answer at
+    <https://docs.uppmax.uu.se/cluster_guides/modules/>,
+    where the module system is explained
+
+- Search the module system for a tool called `cowsay` to find out
+  in which module it is installed
+
+???- question "Answer"
+
+    Use `module spider` to search:
+
+    ```bash
+    module spider cowsay
+    ```
+
+- Load the latest version of the module for `cowsay`
+
+???- question "Answer"
+
+    After having used `module spider cowsay`, we've seen that the
+    latest version is `3.03`. Hence we load the module like this:
+
+    ```bash
+    module load cowsay/3.03
+    ```
+
+- To confirm `cowsay` works, type `cowsay hello`. A cow that says 'hello'
+  should appear
+
+- Unload the module for `cowsay`
+
+???- question "Answer"
+
+    One does not need to add a version to unload a module:
+
+    ```bash
+    module unload cowsay
+    ```
+
+???- question "Answer"
+
+- Confirm that `cowsay` does not work anymore,
+  by typing `cowsay hello`. This should give an error
+
+### Exercise 4: the `bioinfo-tools` module
+
+Go to the UPPMAX documentation at
+[https://docs.uppmax.uu.se](https://docs.uppmax.uu.se),
+then answer these questions:
+
+- Load the `samtools` module, without loading the `bioinfo-tools` module
+  (if you have loaded it, unload it).
+  Which error message do you get?
+
+???- question "Answer"
+
+
+    <!-- Indeed, line lengths beyond 80 characters -->
+    <!-- markdownlint-disable MD013 -->
+
+    ```bash
+    [sven@rackham1 ~]$ module load samtools
+    Lmod has detected the following error:  These module(s) or extension(s) exist but cannot be loaded as requested: "samtools"
+       Try: "module spider samtools" to see how to load the module(s).
+    ```
+
+    <!-- markdownlint-enable MD013 -->
+
+
+- Do what is suggested, that is, do `module spider samtools`. Is the
+  suggestion to load `bioinfo-tools` given there?
+
+???- question "Answer"
+
+    No:
+
+    <!-- Indeed, line lengths beyond 80 characters -->
+    <!-- markdownlint-disable MD013 -->
+
+    ```bash
+    [sven@rackham1 ~]$ module spider samtools
+
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+      samtools:
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+         Versions:
+            samtools/0.1.12-10
+            samtools/0.1.19
+            samtools/1.1
+            samtools/1.2
+            samtools/1.3
+            samtools/1.4
+            samtools/1.5_debug
+            samtools/1.5
+            samtools/1.6
+            samtools/1.8
+            samtools/1.9
+            samtools/1.10
+            samtools/1.12
+            samtools/1.14
+            samtools/1.16
+            samtools/1.17
+            samtools/1.19
+            samtools/1.20
+         Other possible modules matches:
+            SAMtools
+
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+      To find other possible module matches execute:
+
+          $ module -r spider '.*samtools.*'
+
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+      For detailed information about a specific "samtools" package (including how to load the modules) use the module's full name.
+      Note that names that have a trailing (E) are extensions provided by other modules.
+      For example:
+
+         $ module spider samtools/1.20
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+    ```
+
+    <!-- Indeed, line lengths beyond 80 characters -->
+    <!-- markdownlint-enable MD013 -->
+
+
+- Do `module spider samtools` to get help about the latest version. Is the
+  suggestion to load `bioinfo-tools` given there?
+
+???- question "Answer"
+
+    Yes:
+
+    <!-- Indeed, line lengths beyond 80 characters -->
+    <!-- markdownlint-disable MD013 -->
+
+    ```bash
+    [sven@rackham1 ~]$ module spider samtools/1.20
+
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+      samtools: samtools/1.20
+    -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+        You will need to load all module(s) on any one of the lines below before the "samtools/1.20" module is available to load.
+
+          bioinfo-tools
+     
+        Help:
+           samtools - use samtools 1.20
+          
+           Version 1.20
+    ```
+
+    <!-- markdownlint-enable MD013 -->
+
+Remember, whenever you cannot find something, do:
+
+```bash
+module load bioinfo-tools
+```