[Bioperl-l] Cleanup of BioPerl distribution website
cjfields at uiuc.edu
Sun Sep 17 00:01:27 EDT 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.
> 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.
>> On Sep 16, 2006, at 4:03 PM, Nathan S. Haigh wrote:
>>> Mauricio Herrera Cuadra wrote:
>>>> I've done the initial moves and created new signature files for
>>>> 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?)
>>> 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
>>> 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
>>> one then probably needs to be created for the old_releases
>>> 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!
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> 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
> MAURICIO HERRERA CUADRA
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
More information about the Bioperl-l