[Bioperl-l] bioperl-live CVS installation

[Heikki Lehvaslaiho]

On Thursday 29 September 2005 14:56, Paul G Cantalupo wrote:
> Hello,
>
> I am using the CVS bioperl-live repository and trying to understand how to
> properly use CVS. After I typed 'cvs update', I got the following:
>
> ? Makefile
> ? blib
> ? pm_to_blib
> ? maintenance/symlink_scripts.pl
> cvs update: Updating .
> cvs update: Updating Bio..............
>
> Is it necessary to delete the files/directories that are preceeded with a
> question mark (?) before 'cvs update'?

No. It just means that cvs is agnostic about those files.

Since you seem to be new to cvs: you can silence cvs to some extent to better 
see the changes:

> cat /home/heikki/.cvsrc
cvs -q
diff -c
update -dP

-d to update is important as it tells update to:

"Create any directories that exist in the repository if they're missing from 
the working directory. Normally, update acts only on directories and files 
that were already enrolled in your working directory. "


> Also, after I perform a 'cvs update', is it necessary to run the usual:
>
>    perl Makefile.PL
>    make
>    make test
>    make install
>

Not necessary. The only necessary step is to point perl to the installation 
directory, e.g.:

export PERL5LIB='$HOME/src/bioperl-live:$HOME/src/bioperl-run' 
(in your ~/.bach_profile)

However, it is recommendable to run the first to see what CPAN modules you 
might be missing to use some specific functionality. (and 'make test' if you 
want to help testing the code, of course)


 -Heikki


> Thank you,
>
> Paul
>
> Paul Cantalupo
> Research Specialist/Systems Programmer
> 559 Crawford Hall
> Department of Biological Sciences
> University of Pittsburgh
> Pittsburgh, PA 15260
> Work: 412-624-4687
> Fax: 412-624-4759
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
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