[Bioperl-l] newbie wants install help

Malay mbasu at mail.nih.gov
Fri Aug 10 11:25:35 EDT 2007

hari jayaram wrote:
> Hi I am trying to install bioperl as a non root user since I dont have root
> access on the machine.
> I was following the instructions as given on the wiki at
> http://bioperl.open-bio.org/wiki/Installing_Bioperl_for_Unix
> I started from scratch using perl version v5.8.5 and used cpan to install
> the bioperl module prerequisites bundle Bundle::BioPerl since I thought it
> was needed. Everything worked just fine
> I could use cpan as a non root user following instructions given at
> http://www.dcc.fc.up.pt/~pbrandao/aulas/0203/AR/modules_inst_cpan.html
> But when I try to install bioperl using the instructions for non-root I get
> an error when I build Module::Build because I am not root.
> Iget the same Module::Build error when I try to install without CPAN using
> command line script perl Build.PL --install_base option as given on the
> wiki.
> Is there a way out
> Thanks for your help in advance
> harijay
> Brandeis University

This is related your situation and broadly applicable to all perl users 
in a non root situation. I can tell from my own experience the best way 
to handle your situation is to use your own Perl, if you are a dedicated 
perl developer. Just compile and install your own perl installation in 
any directory of you choice and put the "bin" directory in front of you 
path and off you go. The advantages are several fold. First, you get a 
very optimized, fast perl. The sysadmin might have just installed a 
binary run-of-the-mill perl version. Second, you get all the freedom of 
installing the very latest updates of all the modules. The sysadmins may 
be too busy man to update perl frequently. Third, a very common problem 
with production machine is that they follow strictly the perl 
installation instruction and avoid threaded perl, which clips your wings 
particularly, when almost all machines contain multiple processors.

The drawbacks are related to finding "/usr/bin/perl" in the shebang 
line. If you follow the perl way of installing any script, it will take 
care of it. When you develop, use the more portable way of

#!/usr/bin/env perl
BEGIN {$^W =1 } # Use it switch on compile time warnings (-w)

All the best,


Malay K Basu

More information about the Bioperl-l mailing list