3.3.5. Using installed modules

Using included commands

If the module includes commands, those will be installed in $HOME/perl5/bin. This directory will be included in $PATH, when you configured local-lib. Hence, you can start using the commands included in a module immediately after installation.

For example, here is the help page of the fasuniq command included with the FAST package installed in the previous step:

fasuniq -h
Usage:
    fasuniq [options] [MULTIFASTA-FILE]

    [MULTIFASTA-DATA-ON-STDIN] | fasuniq [options]
...

Using modules in your scripts

Modules will be installed in:

$HOME/perl5/lib/perl5/5.30.0.

Note

This is the module path for Perl 5.30.0.

It you have a different version of Perl installed on your system, it will change.

As local-lib makes these modules discoverable automatically, you can start using them in your scripts immediately.

Here is an example using the Bio::Phylo package. After installing the module with cpanm Bio::Phylo, create a file using a text editor and copy the following content:

use Bio::Phylo;

# print version
print Bio::Phylo->VERSION;

# print citation
print Bio::Phylo->CITATION;

Save the file as biophylo_test.pl and then run it:

perl biophylo_test.pl

Output:

v2.0.1Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011.
Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63.
doi:10.1186/1471-2105-12-63