[Bioperl-l] bioperl-live install issue on unix

Dave Messina David.Messina at sbc.su.se
Wed Dec 10 07:36:46 EST 2008

Following on to what Dave H. said, cpan itself needs to know that you want
to install in a personal module area; it, too, defaults to the system

>From the CPAN man page:
 5)  I am not root, how can I install a module in a personal directory?

           You will most probably like something like this:

             o conf makepl_arg "LIB=~/myperl/lib \
                               INSTALLMAN1DIR=~/myperl/man/man1 \
             install Sybase::Sybperl

           You can make this setting permanent like all "o conf" settings
with "o conf commit".

           You will have to add ~/myperl/man to the MANPATH environment
variable and also tell your perl programs to look into
           ~/myperl/lib, e.g. by including

             use lib "$ENV{HOME}/myperl/lib";

           or setting the PERL5LIB environment variable.

           Another thing you should bear in mind is that the UNINST
parameter should never be set if you are not root.

So, now that you've wiped your cpan configuration parameters, you need to
set some new ones, even before you update CPAN.

Actually, the advice on the BioPerl Installation page is better than the
above. Do the following:

% cpan
cpan>o conf makepl_arg PREFIX=/home/users/dag/My_Local_Perl_Modules
cpan>o conf mbuildpl_arg "--prefix /home/users/dag/My_Local_Perl_Modules"
cpan>o conf commit

Here's the whole section of the installation instructions that deal with
personal installations:

By the way, just a bit below that section are the instructions on how to set
your PERL5LIB environmental variable.


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