[Bioperl-l] Using a bioperl cvs checkout

[Allen Day]

in a calling perl script you can add a line like:

use lib 'path/to/bioperl-live';

and it will take precedence over PERL5LIB / PERLLIB / @INC / etc.

or you can do it like this (my preferred method for using an alternate lib 
for a one-off:

perl -Ipath/to/bioperl-live path/to/myscript.pl

this basically puts the '-I' argument into the 0th slot of @INC so it gets 
used first.  you can give multiple '-I' args if needed.

-Allen


On Tue, 11 Jan 2005, Barry Moore wrote:

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