Perl

Introduction

Perl has been one of the cornerstones of bioinformatics and is unlikely to give up this role, simply because so many user-contributed modules are avaiable for it.

Best way to install modules

This clearly cpanm, but it has be installed first. However, this is remarkably easy and does not need the clunky cpan interface:

curl -L https://cpanmin.us | perl - --sudo App::cpanminus

Then to keep account of the modules you have, you can use

cpan -l

This is useful when you have one perl installation in which you have gradually installed many modules and, when installing a new version of perl, you want o install all of these in one go by piping to cpanm. However, bear in mind when you do this, that many modules may need special libraries and there could be very many failures. Nevertheless this method will still install a good deal of the libraries that otherwise would be tedious to install one by one.

And then to actually install the outdated modules, you first have to

cpanm App::cpanoutdated

and then

cpan-outdated -p | cpanm

Installation

New versions of perl follow this configuration before compiling

sh Configure -de -Dprefix=/shelf/modulefiles/tools/perl/5.26.1 -Duseshrplib

As well as installing in the right place, it will also create the perl shared library, which other programs, those who like to sport perl interfaces, might like to use.