[Bioperl-l] Using a bioperl cvs checkout

[Brian Osborne]

Barry,

By setting PERL5LIB to some directory you're telling Perl to search that
directory first when searching for the module or modules in question. So
yes, Perl will have at least 2 directories in its @INC variable but it will
use the modules it finds first, in PERL5LIB, and ignore the rest. This is
analogous to how the OS treats the PATH variable. I commend you on your
clever setup, you have the best of both worlds this way.

Brian O.


105 ~>perl -e 'print @INC'
/usr/lib/perl5/5.8.2/cygwin-thread-multi-64int/usr/lib/perl5/5.8.2/usr/lib/p
erl5
/site_perl/5.8.2/cygwin-thread-multi-64int/usr/lib/perl5/site_perl/5.8.2/usr
/lib
/perl5/site_perl

106 ~>setenv PERL5LIB /fake

107 ~>perl -e 'print @INC'
/fake/usr/lib/perl5/5.8.2/cygwin-thread-multi-64int/usr/lib/perl5/5.8.2/usr/
lib/
perl5/site_perl/5.8.2/cygwin-thread-multi-64int/usr/lib/perl5/site_perl/5.8.
2/us
r/lib/perl5/site_perl


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Barry Moore
Sent: Tuesday, January 11, 2005 5:05 PM
To: Hilmar Lapp
Cc: bioperl
Subject: [Bioperl-l] Using a bioperl cvs checkout


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
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>

--
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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