[Bioperl-l] bioperl installation problems with External Modules - doesn't see installed modules

s.rayner at att.net s.rayner at att.net
Thu Jan 26 00:58:42 EST 2006

I am trying to install the bioperl::bundle to use some of the external perl modules. 
Particularly the bio::DB::GFF module for use with biodas.

I follow the instructions, both from the bioperl web site for installing the bioperl bundle, and also specific instructions from the biodas web site for installing bio::DB::GFF.  Namely

   (1) Make sure that CVS is installed on your system.

    (2) Use the following command (all on one line) to login to the server

         % cvs -d :pserver:cvs at cvs.bioperl.org:/home/repository/bioperl login

          when prompted, the password is 'cvs'

    (3) Check out the bioperl package you are interested in, for most
    users this will be the bioperl-live source tree.  The following
    command should be executed as one line.

         % cvs -d :pserver:cvs at cvs.bioperl.org:/home/repository/bioperl checkout bioperl-live

    The login and checkout procedure should only have to be done
    once. To update the source directories in the future it should be
    possible just to enter the top level directory and issue the
    following command:

         % cvs update

This will create the directory ``bioperl-live''. Now build and install bioperl with the following recipe:

         % cd bioperl-live
         % perl Makefile.PL
         % make
         % make test
         % make install

The last step will probably need to be run as root.

When i perform either of these steps i get the message that the installation was successful, but bioperl and biodas return a message that the modules have not been installed.

They are physically present on the disk, but the programs don't seem to know where to find them.

Can anyone suggest how to fix this problem?



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