[Bioperl-l] How to install CPAN's modules needed by BioPerl

[Wiepert, Mathieu]

See posts from Jason Stajich and Chris Dagdigian from Monday 3/24.

Subject was
Is there a way to manually install Bundle::BioPerl


Cut and paste of Jason's post...()

-----Original Message-----
From: Jason Stajich [mailto:jason at cgt.mc.duke.edu]
Sent: Monday, March 24, 2003 6:36 PM
To: John Dayton
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Is there a way to manually install
Bundle::BioPerl


You can provide the cpan shell with a make arguments, specifically
LIB=$HOME/lib/perl which will allow you to install modules in a private
directory.

cpan> o conf makepl_arg LIB=$HOME/lib/perl
will be temporary for the session, I don't remember how to make it
permanent - although you can set it during the CPAN configuration, just
blow away your .cpan directory and you should get asked about config
options again.

Also from the CPAN perldoc
       5)  I am not root, how can I install a module in a per-
           sonal directory?

           You will most probably like something like this:

             o conf makepl_arg "LIB=~/myperl/lib \
                               INSTALLMAN1DIR=~/myperl/man/man1 \
                               INSTALLMAN3DIR=~/myperl/man/man3"
             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 envi-
           ronment 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.

On Mon, 24 Mar 2003, John Dayton wrote:

> Hi,I have been bother by this problem for long time
> and I will appreciate a lot if someone may help me
> out.
>
> Since I don't have root permission on my computer,so I
> can't use Bundle::BioPerl CPAN bundle to automatically
> fectch and install the necessary modules for bioperl
> need.
>
> I have tremendous trouble when trying to getting each
> individual modules needed by bioperl(e.g. IO::string)
> and install it to my private space.Although I have
> accordingly change the directory in my program,it
> always shows that IO::string is not installed.
>

> Can anyone give me any suggestion about how I can use
> CPAN bundle to automatically installed all modules
> into my private space OR how I can get those modules
> work individually?
>
Make sure the your private directory is available to perl and added
through the env variable PERL5LIB.  You can check this by running
perl -V

If your specific directory where the modules are installed do not show up
then it won't work.

> Thanks a lot for your kindly help!
>
> John
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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-----Original Message-----
From: ying lin [mailto:ylin at mail.eecis.udel.edu]
Sent: Wednesday, March 26, 2003 11:00 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] How to install CPAN's modules needed by BioPerl


Hi,all

I am new comer for bioperl.Please bear with my stupid questions.

I have difficulties trying to install CPAN's packages needed by
bioperl.But I can't easily install them via the Bundle::BioPerl CPAN
bundle as this automatic installation requires that I have root permission
while I don't.

So is there any way to change the installation of CPAN bundle to my
private space where I have writting permission?Or do I need to install all
the CPAN's packages one by one manually?

What's your experience?Thanks a lot for your help.

Ying
Dept. of Computer Science
Univ. of Delaware

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