CSC Computing Environment

Perl

💬 Perl scripts and applications do not need installation. They can be simply downloaded and run.

💬 To run Perl applications, it usually best to first load a Perl module.

☝🏻 A system Perl installation is available (without a module), but it is very barebones and is missing many commonly used libraries.

1. To check available module versions, use:

module spider perl

2. The current default version is 5.34.1 and can be loaded with:

module load perl

☝🏻 To ensure scripts use the intended Perl version after loading a module you should either call the script with perl:

perl my_app.pl

or make sure the shebang line of the script is:

#!/usr/bin/env perl

Installing Perl modules

💬 Sometimes applications may require additional modules to run.

• These “perl modules”, should not be confused with the software modules on CSC supercomputers.

💬 You should check the installation instructions for each module. For libraries in CPAN, the easiest method is to use cpanm.

• You can check out the CPAN documentation here.

In this example, we’ll add the perl module JSON to our own environment

1. Check if JSON is already available:

perl -e 'use JSON;'

• The error message indicates that it is not found, so you need to install it.

🗯 By default, cpanm tries to install new modules to the Perl installation path, which will not work.

• You need to set the location to a directory where you have write access. It could be e.g. your project’s /projappl directory.
• This is accomplished by setting a few environment variables.

2. Replace the desired path for PERL_BASE and run the following:

export PERL_BASE="/projappl/<project>/$USER/myperl"    # example, replace <project> with your CSC project, e.g. project_2001234
export PERL_MM_OPT="INSTALL_BASE=$PERL_BASE"
export PERL_MB_OPT="--install_base $PERL_BASE"
export PERL5LIB="$PERL_BASE/lib/perl5"

3. You can now install the module. In this case, it is in CPAN, so you can use cpanm:

cpanm JSON

4. To use the module, you need to tell Perl where to find it. In this case, you can set the $PERL5LIB environment variable (already done above):

export PERL5LIB="/projappl/<project>/$USER/myperl/lib/perl5"    # replace <project> with your CSC project, e.g. project_2001234

5. You can now try again:

perl -e 'use JSON;'

• This time there’s no error message, indicating that the JSON module is now available.

Additional info

💬 The installation only needs to be done once, but you need to always ensure Perl knows where to find the installed modules.

💭 There are three main ways to do this (we used the second already):

Option 1

• Pass the path using the command-line option -I:

perl -I /projappl/<project>/$USER/myperl/lib/perl5 ./my_app.pl    # replace <project> with your CSC project, e.g. project_2001234

Option 2

• Include the path in the $PERL5LIB environment variable:

export PERL5LIB=/projappl/<project>/$USER/myperl/lib/perl5:$PERL5LIB    # replace <project> with your CSC project, e.g. project_2001234

Option 3

• Include the path in your Perl script with use lib

use lib '/projappl/<project>/$USER/myperl/lib/perl5';
use My::Module;

Bioperl

💬 If you need the BioPerl collection of Perl modules, you can find this pre-installed on Puhti (try module spider bioperl).

💡 See our BioPerl documentation for more details.

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