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.
- To check available module versions, use:
module spider perl
- 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
- 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.
- 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"
- You can now install the module. In this case, it is in CPAN, so you can use
cpanm
:
cpanm JSON
- 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
- 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.