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The module system

Learning objectives

  • Practice using the UPPMAX 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
  • Extra: Can find pre-installed software from the documentation
  • Extra: Can find pre-installed databases from the documentation
For teachers

Teaching goals are:

  • Learners have practiced using the UPPMAX 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
  • Extra: Learners have found pre-installed software from the documentation
  • Extra: Learners have found pre-installed databases from the documentation

Lesson plan:

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 Bianca?
  • 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:

module load bioinfo-tools

Only after loading it will some other tools appear.

Exercises

Need a video?

Here is a video that shows the solution of these exercises

flowchart TD

  classDef minimal_node fill:#fdd,color:#000,stroke:#f00
  classDef extra_node fill:#ffd,color:#000,stroke:#ff0

  exercise_1[1.work with modules]:::minimal_node
  exercise_2[2.the bioinfo-tools module]:::minimal_node
  exercise_3[3.find the software]:::extra_node
  exercise_4[4.find the databases]:::extra_node

  exercise_1 --> exercise_2 --> exercise_3 --> exercise_4

Exercises for this session. Red nodes: minimal, needed in other sessions. Yellow nodes: extra, useful in general.

Exercise 1: work with modules

Go to the UPPMAX documentation at https://docs.uppmax.uu.se, then answer these questions:

  • Find the UPPMAX documentation on modules
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
Answer

Use module spider to search:

module spider cowsay
  • Load the latest version of the module for cowsay
Answer

After having used module spider cowsay, we've seen that the latest version is 3.03. Hence we load the module like this:

module load cowsay/3.03

  • To confirm cowsay works, type cowsay hello. A cow that says 'hello' should appear

  • Unload the module for cowsay

Answer

One does not need to add a version to unload a module:

module unload cowsay
Answer
  • Confirm that cowsay does not work anymore, by typing cowsay hello. This should give an error

Exercise 2: the bioinfo-tools module

Go to the UPPMAX documentation at 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?
Answer 

[sven@bianca1 ~]$ 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).
  • Do what is suggested, that is, do module spider samtools. Is the suggestion to load bioinfo-tools given there?
Answer

No:

[sven@bianca1 ~]$ 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
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

  • Do module spider samtools to get help about the latest version. Is the suggestion to load bioinfo-tools given there?
Answer

Yes:

[sven@bianca1 ~]$ 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

Remember, whenever you cannot find something, do:

module load bioinfo-tools

Extra: Exercise 3: find the software

Go to the UPPMAX documentation at https://docs.uppmax.uu.se, then answer these questions:

  • Find to list of installed software. Estimate how many pieces of software are installed on Bianca
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

Extra: Exercise 4: find the databases

Go to the UPPMAX documentation at https://docs.uppmax.uu.se, then answer these questions:

  • Find to list of databases. Estimate how many collections of databases are installed on Bianca
Answer

One can find the answer at http://docs.uppmax.uu.se/databases/overview/, where one can find around 7 collections of databases installed.