[Bioperl-l] Partial BioPerl installations

[john herbert]

Please ignore my last question, I looked up what the PERL5LIB variable
does. Sorry, John.

>>> "john herbert" <john.herbert at clinical-pharmacology.oxford.ac.uk>
02/03/2004 16:24:22 >>>
Thanks for the info Heikki, very helpful.
One question arises, could I change the Perl library location to my
own
custom location instead of PERL5LIB?

Thanks,

John.

>>> Heikki Lehvaslaiho <heikki at ebi.ac.uk> 02/03/2004 16:11:26 >>>
John,

This s something that have been discussed but no definite action has
been 
taken. Bioperl core is still one monolithic package. However, if you
really 
are tight with space there are some things you can do.

I am assuming you are using anonymous CVS access and setting PERL5LIB
to point 
your perl to the bioperl modules. The whole bioperl core takes ~25M. 

1. Remove everything else that CVS and Bio subdirectories. This takes
the disk 
space down to 12M. Run 'cvs update' within the Bio directory and you
can keep 
up to date.  If you need to run tests, examples or read documentation,
you 
can do 'cvs update' in the main directory.

2. If all you need is the basic sequence manipulation classes, you
can,

possibly, remove a number of subdirectories under Bio. For example, if
you do 
not directly need  these, could try removing them:

CodonUsage
Coordinate
Das
Graphics
LiveSeq
Map
MapIO
Matrix
Ontology
Phenotype
PopGen
Tree
TreeIO
Variation

Note that I am only guessing here. If you try removing these, keep a
log and 
be prepared to restore modules from cvs. If you really try this,
please

report back to the list. We'd be interested in knowing if and what
works.

Yours,

	-Heikki

On Tuesday 02 Mar 2004 14:45, john herbert wrote:
> Hello.
> Is there away to only install specific parts of BioPerl on to your
> system. My problem is I have limited space on my machine and
therefore
> don't want to install the whole of BioPerl if I am only going to use
> certain objects.
>
> I realise some classes will have super classes and all will have to
be
> installed but I am assuming this will not need a full BioPerl
install.
>
> Any information on how I could install just specific classes from
> BioPerl would be much appreciated, thank you.
>
> Kind regards,
>
> John Herbert,
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org 
> http://portal.open-bio.org/mailman/listinfo/bioperl-l 

-- 
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     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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