[Bioperl-l] Using a bioperl cvs checkout

[Barry Moore]

Hilmar (or others)-

The bioperl cvs documentation was great, and I've managed to checked out 
bioperl-live, bioperl-db and bioperl-run from anonymous cvs into a 
directory off of my home.  Now I've got a couple of questions about how 
to best utilize this code from cvs.  I've got an existing installation 
of bioperl 1.4 which I probably don't need to duplicate, but I'm unsure 
of what is the best way to utilize the code from cvs.  I see that the 
cvs checkout comes with Makefile.PL etc. Should I run make process on 
the cvs checkout and let it install everything into my standard perl 
library location, or should I keep my cvs checkouts seperate and tell 
perl where it is?  I don't have a developer account on bioperl cvs, so I 
won't be commiting (or even changing my local copy) at this point, but I 
might as well do things the right way and from reading 'Open Source 
Development with CVS' it seems like I ought to be using the cvs checkout 
without 'installing' it or moving it anywhere.  If I keep them seperate 
the bioperl cvs docs suggest to export PERL5LIB='$HOME/src/bioperl' . If 
I do that I think perl will see two copies of the bioperl modules when I 
run a script (the cvs copy and the installed 1.4 copy).  How do I know 
which copy of the modules a script will be using?  I don't want to 
completely do away with the system installation of bioperl 1.4 because 
another user is using that.

Barry

Hilmar Lapp wrote:

> Did the test script that you ran come with bioperl? Bio::DB::BioDB 
> comes with bioperl-db, and is not needed for anything else. Also, 
> bioperl-db is not included in the bioperl 1.4 distribution. If you 
> want it, you do need to obtain from CVS at this point. Let me know if 
> you have problems with that.
>
> Also, if you do want to use bioperl-db I do recommend you obtain 
> bioperl 1.4 from the CVS branch as well, or otherwise wait for the 1.5 
> release. The 1.4.0 release has problems in the interpro and GO 
> ontology parsers, and 1.4.1 was never released in anticipation of 1.5.
>
>     -hilmar
>
> On Jan 10, 2005, at 5:10 PM, Barry Moore wrote:
>
>> I've just installed bioperl 1.4 (bioperl-core, bioperl-run and 
>> bioperl-db) on a new system (Debian woody). I run a test script that 
>> works fine on my old system and get an error that BioDB.pm can't be 
>> found.  Sure enough BioDB.pm isn't on my new system, but it is on the 
>> old (also bioperl 1.4 Debian woody).  I look in cvs and BioDB.pm is 
>> there, but I look in the distribution downloaded from bioperl.org and 
>> it seems to be missing BioDB.pm and several other files?  I can get 
>> the files from cvs, but is this an error in the distribution file?
>>
>> Barry
>>
>> -- 
>> Barry Moore
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT
>>
>>
>>
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-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT