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perlmoduleinstallationbioperl

Install BioPerl with custom library path

I tried to install a new version of BioPerl on my PC without root and get errors concerning too old versions of required modules. So I installed them into a custom directory.

Is there a possibility to set up a library parameter next to --install_base for the installation? README and INSTALL instructions just provide it for an installation using cpan, which is no option for me.

thanks

My attempts:

my $dir=catdir('home','user','my','bioperl');
my $lib=catdir('home','user','my','lib');
push @INC , $lib;
$lib=$lib.':'.$_ for @INC;

1.

system("cd tools/BioPerl-1.6.923 && perl Build.PL --install_base $dir && ./Build test && ./Build install");

2.

system("export EXPATLIBPATH=$lib && cd tools/BioPerl-1.6.923 && perl Build.PL --install_base $dir && ./Build test && ./Build install");

3.

system("export PERL5LIB=$lib && cd tools/BioPerl-1.6.923 && perl Build.PL --install_base $dir && ./Build test && ./Build install");
Solution

  • Being without root access is a common issue, that's why there is perlbrew.

    \curl -L http://install.perlbrew.pl | bash

    Then just install cpanminus for use with perlbrew: Installing to local perl (perlbrew).

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

    That should enable you to have a stable environment for installing all your modules including Bio::Perl. Could just do the following or also read How do I install the latest BioPerl version when using perlbrew?

    cpanm Bio::Perl