Software and tools

Objectives

We’ll briefly get overviews over
- software tools on UPPMAX
- databases
Introduction guide for installing own software or packages
Very short introduction to developing own programs

Instructor note

Approx timing: 13:00-13:30
Theory and type-along

800+ programs and packages are installed.
To avoid chaos and collisions, they are managed by a module system.
This system keeps installed software hidden by default, and users have to explicitly tell their terminal which version of which software they need.
The modules are most often available across cluster (except for Miarka)

Note

Bioinformatics tools require loading the “bioinfo-tools” module first.

Modules

Modules

Installed software

You can also find (almost) all installed software at: https://www.uppmax.uu.se/resources/software/installed-software/

Hands on using a tool

use matlab

$ matlab &

Does not work!
Load module first

$ module avail matlab

module load matlab will start Default version (often latest) demarked with a D in the list
Let’s load a specific version, often good for reproducibility.

$ module load matlab/R2020b

$ matlab &

Matlab starts (if X11 is active)

use Samtools

$ module load samtools

        "These module(s) or extension(s) exist but cannot be loaded as requested: "samtools""

$ module load bioinfo-tools samtools

Bioinformatic tools are hidden by default

Installed databases

Installed databases at UPPMAX

Run own scripts or programs

Unless your script or program is in the active path, you run it by the full path or ./<file> if you are in the present directory.

Demo: Run a Fortran program

Run the program “sunray” located in: /proj/introtouppmax/labs/sunray

Solution

2 alternatives

 /proj/introtouppmax/labs/sunray
 
 cd /proj/introtouppmax/labs/
 ./sunray

Keypoints

Centrally installed software are reached through the module system and available throughout all nodes.
Your own installed software, scripts, python packages etcetera are available from their paths.