[Bioperl-l] Bioperl Server Reconfig

Nathan Haigh n.haigh at sheffield.ac.uk
Mon Oct 16 16:39:02 UTC 2006

Sendu Bala wrote:
> Nathan Haigh wrote:
>> Mauricio Herrera Cuadra wrote:
>>> Done. Could you please check if it works as it should?
>>> Cheers,
>>> Mauricio.
>> Will do as soon as I have created a Bioperl 1.5.2-rc1 PPD and got
>> someone to pop it in http://bioperl/DIST
>> Volunteers?
> I'm sure Mauricio would be happy to do it, but so am I. You may want
> to hold off a little while until I release rc2, which may be a few
> hours away.

Just e-mailed Mauricio links to the files off list, It's not a big job
for me to remake the bioperl PPD, so Mauricio it's up to you if you want
to wait 18hrs for me to make the PPDs for 1.5.2-rc2.
>> BTW, was it agreed to have Bundle::BioPerl as a prereq of Bioperl for
>> the PPD? I seem to remember that there was talk about having to maintain
>> a separate Bundle::BioPerl for each release of Bioperl. Any ideas on
>> this front?
> It depends on what is in the PPD and what kind of auto-dependency
> features the ActiveState installer has. Given Perl 5.8 and your
> current PPD, does Bioperl install with the same or fewer number of
> skips if you also install Bundle::BioPerl first? That is, does
> Bundle::BioPerl even do anything useful anymore? If not, obviously
> don't bother making it a pre-req. If it does, my opinion is that you
> make it a pre-req. If people really don't want to install the optional
> stuff they can download the .zip file and install manually without
> even a make.
As far as the PPDs are concerned - no tests are run during installation.
PPM more or less just copies files into the correct place for Perl to
find so both approaches result in the same thing. However, I've not
tried making a CPAN distribution file for either Bioperl or
Bundle::Bioperl - I wouldn't know where to start!

MakeFile.PL now only documents the prereq in one place (%packages), and
this is used to add the prereq to the bioperl PPD when issuing "nmake
ppd". This way, each release of BioPerl should be up-to-date with prereq
as long as developers add their modules prereq to %packages. If we have
Bundle::BioPerl, most of those prereq need to be moved from the Bioperl
PPD to the Bundle::BioPerl PPD - a bit of a pain because there are no
guidelines as to what should/should not go in Bundle::BioPerl.
Therefore, as far as the PPDs are concerned, it far easier to do away
with Bundel::BioPerl.


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