[Bioperl-l] Cleanup of BioPerl distribution website

Chris Fields cjfields at uiuc.edu
Sun Sep 17 04:01:27 UTC 2006


I personally don't have a problem with the changes.  Bioperl 1.5 had  
serious problems anyway.  It's a shame we don't have a 1.5.1 ppm but  
when we release 1.5.2 we'll add one to DIST.  Nathan, what do you think?

When I make up a local ppm package for installation on WinXP, I  
maunally edit the XML generated (the ppd file) to make it more  
consistent with my local distribution, including modifying the  
prereqs.  I think we can also include an installation script with the  
ppm (which I haven't played around with, but Scott Cain has done this  
with the Generic Genome Browser PPM package).  When we start making  
release candidates I can try packaging everything up for Windows and  
have you add it to the main directory, then modify the package.lst to  
point to the newer ppms as well as Text::ShellWords and GD::SVG.  We  
can have the old package.lst (in old_releases) point at the older  


On Sep 16, 2006, at 9:33 PM, Mauricio Herrera Cuadra wrote:

> Nathan & Chris,
> I've taken a look into Bioperl.ppd and it uses bioperl-1.5- 
> ppm.tar.gz which according to the ppd file corresponds to the 1.5.0  
> release, so I renamed Bioperl.ppd to Bioperl-1.5.ppd and moved both  
> of them into 'old_releases'.
> I've also edited all ppd files in 'old_releases' to modify their  
> CODEBASE HREF's to the new locations. Copied package.lst into  
> 'old_releases' and modified this also.
> The original package.lst in 'DIST' was copied to package.lst.old as  
> a backup, so I could edit the first one to reflect directory moves.  
> Also generated new signature files for both directories.
> Please take a look and tell me if all of this changes make sense.
> Cheers,
> Mauricio.
> Chris Fields wrote:
>> There was a post on list recently about problems using the newer  
>> PPM  GUI that comes with ActivePerl 5.8.819 (it wanted to  
>> downgrade all  installed prereq modules already installed).  I  
>> haven't tried it  myself.  I did find that the newer bioperl PPM  
>> (v. 1.5) didn't show  up when I last used the command-line PPM for  
>> ActivePerl 5.8.817, so  maybe package.lst needs to be updated.
>> We can probably leave the PPM related stuff for now.  I'm not  
>> sure  whether anyone would be interested in having access to the  
>> older ones  but we could probably make them available in the sub  
>> directory with a  modified package.lst.
>> We'll try getting a PPM for Windows for the next developer  
>> release  and add it then.
>> Chris
>> On Sep 16, 2006, at 4:03 PM, Nathan S. Haigh wrote:
>>> Mauricio Herrera Cuadra wrote:
>>>> Chris,
>>>> I've done the initial moves and created new signature files for  
>>>> each
>>>> directory. Currently I've doubts on what to do with the  
>>>> following  files:
>>>> - Bioperl.ppd            (what does this stands for?)
>>>> - GD-SVG-0.25-ppm.tar.gz (where does this came from?)
>>>> - GD-SVG.ppd             (where does this came from?)
>>>> - bioperl-1.5-ppm.tar.gz (1.5.0 or 1.5.1 release?)
>>>> - package.lst            (still in use? needs updating? be   
>>>> splitted into
>>>>                            corresponding subdirectories?)
>>>> Cheers,
>>>> Mauricio.
>>> Bioperl.ppd and bioperl-1.5-ppm.tar.gz are the files required  
>>> for  users
>>> wishing to install Bioperl 1.5 via ppm (i.e. mainly windows  
>>> users).  The
>>> same is true for GD-SVG* files which allow these users to install  
>>> this
>>> module which if i remember correctly is required by   
>>> Bio::Graphics::*. If
>>> i do remember correctly, this package wasn't available in any of the
>>> standard ppm repositories so was created just for the windows  
>>> ppm  users.
>>> They should probably be kept where they are at least until newer
>>> releases are created for these two modules.
>>> I think package.lst is required by the ppm software to identify the
>>> packages in the current directory/repository. This should be   
>>> updated to
>>> contain only those packages in the same directory as this file. A  
>>> new
>>> one then probably needs to be created for the old_releases  
>>> directory.
>>> Someone may have a better idea of this, especially since ActiveState
>>> have been updating the ppm software etc, so feel free to correct  
>>> me if
>>> needs be!
>>> Cheers
>>> Nathan
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> -- 
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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