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Using software

Using software#

Whenever you want to perform more complex computational tasks, you might use already existing pieces of software. In the most simplified understanding, every command in itself is already considered to be a piece of software. But more commonly, software are understood as bundles of scripts carrying out a series of computational tasks (commands) with many dependencies.

Loading software from a module system#

For widely distributed and commonly used pieces of software (similar to the most common apps that you carry around on your mobile phone), people typically download these from a software repository (analogous to an app store). In our case, we work with a well-maintained module system with pre-installed and continuously updated versions of software. This pre-installed software can thus be loaded from the module system (instead of being installed by every user individually) and automatically loads the required libraries and dependencies to avoid clashes.

# Commands for using the module system
ml or module                # base command; list loaded modules
ml avail                    # list available modules
ml <name> or ml load <name> # load named module
ml unload <name>            # unload named module; after use
ml purge                    # unload all loaded modules
ml spider <name>            # search modules for name

In some cases, people want to install specific software for their own use that is not commonly used by others and thus not available in a pre-installed version on a module system. As you will not be required to install software yourself in this course, we will not cover this but some information is provided in the additional content.

Exercise 2.6#

Exercise 2.6

  • Load the software called Bio from the module system.

# Check whether the software you want exists on the module system
ml B
# Press 'Double-Tab' (press Tab 2x quickly) to show the selection of packages available on the module system

# Load the software that you want
ml Bio

# Run the command (note that it starts with lowercase b)
bio
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