[Bioperl-l] Distribution files, versions

David Messina dmessina at wustl.edu
Fri Nov 10 09:55:44 EST 2006

> bioperl.lisp

This is the emacs template for bioperl module writing. Should be kept  
I think.

> maintenance/symlink_scripts.pl
> maintenance/symlink_scripts.PLS

Don't know if they're still needed, but Makefile.PL still refers to  

> doc/makedoc.PL

I think this does similar to what you propose below, namely  
redefining modules' version strings to be the same as  
Bio::Root::Version's. I don't see any reason to remove it, but I like  
your suggestion to have all the modules get their version from  

> scripts/install_bioperl_scripts.pl

Does what it says. Don't know if it's still needed; I think  
Makefile.PL handles script installation. Re your other post about  
switching over to Build.PL, I think scripts go into /usr/local/bin by  
default, or wherever specified if PREFIX or the like is set when the  
user runs 'perl Makefile.PL'. That seems to fit with other CPAN  
distros' model, and is what I (as an end-user) would expect.


> Most modules in the distribution take their version from
> Bio::Root::Version, but some do not. Is there some reason they must  
> keep
> the version they currently have, or can they be made like the others?
> These are the modules that seem to define their own version (based  
> on a
> quick grep):
> Bio/DB/NCBIHelper.pm
> Bio/DB/Expression/geo.pm
> Bio/DB/EUtilities/elink.pm
> Bio/SeqIO/tinyseq.pm
> Bio/Graphics/Glyph/cds.pm
> Bio/Graphics/Glyph/translation.pm
> Bio/Graphics/Glyph/so_transcript.pm
> Bio/Index/Blast.pm
> Bio/Index/Hmmer.pm
> Bio/Tools/WebBlat.pm
> Bio/Tools/HMM.pm
> Bio/Tools/dpAlign.pm

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