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Re: Intent to package: molecular biology programs

On Fri, 28 Aug 1998, Stephane Bortzmeyer wrote:
bortzm>I'm thinking about packaging for Debian several molecular biology 
bortzm>programs. AFAIK, there is only one, among the hundreds of programs in 


bortzm>daily use by the biologist, which is debianized (Rasmol, by John Lapeyre 
bortzm><lapeyre@physics.Arizona.EDU>). We work here with *many* different 
bortzm>programs, which are typically painful to compile, install, upgrade, 
bortzm>remove, etc. So the Debian system could help.

	I am trying to be eclectic in packaging science things in an
attempt to generate interest.
	Yes, they are hard to package. I thought the same thing. There is
a lot of useful stuff out there that is nearly worthless because a
scientist does not know how to do even a relatively simple port to linux.

bortzm>- most of these programs are awful, from an Unix point of view. No man 
bortzm>pages, no command-line interface ("For such analysis, type 1, for such, 
bortzm>type 2"), horrible coding. It is not seriously possible to clean them, 
bortzm>we'll have to live with it. Is it a reason to exile them in contrib?

	Convert the docs to a  man page, write a short man page refering
to the docs, hound the author for a man page.  I've done all three.

bortzm>- most of these programs have retentive licences, often not because the 
bortzm>author was opposed to free software, but because he thought he was able 
bortzm>to write a licence and the resulting text is both undecipherable and 
	Talk to the author. RMS would perhaps not approve.  But I often
use inclusion on a CD as a selling point to change a license.  A lot of
people are willing to clean up a license.

bortzm>- many programs, since they come from different origins, have the same 
bortzm>name. At least three "scan" executables to put in /usr/bin, besides MH's 
bortzm>scan. Should I create a /usr/gensoft tree, like we do here to prevent 
bortzm>name clashes? (Yes, I know only X11 does that on Debian, but the set of 
bortzm>all biology programs is almost as large.)
	I think not.  I usually rename the programs that clash.  I suppose
others may have thought about better solutions.  The namespace problem  is
only going to get worse.

bortzm>- some of these programs are mostly used with *very* huge databases of 
bortzm>genomes, which are unlikely to be found on any PC (Debian or else) 
bortzm>machine. Anyone here works in biology?

	People bring this up from time to time.  Licenses are also an
issue here. The issue will be forced only when significant numbers of
people use a distribution (Debian) in a field.  I don't know how much
longer the CD will remain the standard medium in its current niche.

John Lapeyre <lapeyre@physics.arizona.edu>
Tucson,AZ     http://www.physics.arizona.edu/~lapeyre

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