[Bioperl-l] CPAN install

Brian Osborne brian_osborne at cognia.com
Wed Feb 25 09:35:11 EST 2004


(1) You're right, there should be instructions in the INSTALL file, I'll fix

(2) That long list of modules from "i/bioperl-1.4/" is the list of modules
in 1.4. If you take a look at the top of that list you'll see "Distribution
id = B/BI/BIRNEY/bioperl-1.4.tar.gz", that's the name you should use, i.e.
"install B/BI/BIRNEY/bioperl-1.4.tar.gz".

However, you'll want to install the Bundle first, "d/BioPerl/" should give
you the exact name.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Dave Howorth
Sent: Wednesday, February 25, 2004 9:06 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] CPAN install

I'm trying to upgrade my bioperl installation to 1.4. I want to do it
from CPAN, using perl -MCPAN because that's the way I install Perl
software. I'm having trouble, so now I have an extra reason: to see if
the install process needs fixing :)  I have a couple of questions:

(1) On <http://www.bioperl.org/Core/Latest/> it says
"Information on how to use CPAN.pm to automatically download BioPerl and
various CPAN module dependencies is described on our INSTALL file." but
the install file <http://www.bioperl.org/Core/Latest/INSTALL> does not
contain this information as far as I can see? (it describes how to
install Bundle::Bioperl that way, but not Bioperl itself)

(2) What is the name of the distribution? The link takes me to
bioperl-1.4 but I get an error when I try to install it:

perl -MCPAN -e shell
cpan> install bioperl-1.4
Warning: Cannot install bioperl-1.4, don't know what it is.
Try the command

     i /bioperl-1.4/

to find objects with matching identifiers.

The suggested search returns a long list of individual modules. I get
similar errors if I try 'bioperl' or 'Bioperl'.

(3) There is a module called Bioperl, which says it is part of the
bioperl-1.4 distribution, but describes itself as "Bioperl 1.3 - Perl
Modules for Biology"

Any ideas?

Thanks, Dave
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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