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Intent to package: molecular biology programs

[Important note: unlike many such announcements here, this one is really 
an intent. I've done almost nothing yet.]

I'm thinking about packaging for Debian several molecular biology 
programs. AFAIK, there is only one, among the hundreds of programs in 
daily use by the biologist, which is debianized (Rasmol, by John Lapeyre 
<lapeyre@physics.Arizona.EDU>). We work here with *many* different 
programs, which are typically painful to compile, install, upgrade, 
remove, etc. So the Debian system could help.

The prime candidates would be Phylip and Clustal (also Blast, may be).

The problems I see:

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

- most of these programs have retentive licences, often not because the 
author was opposed to free software, but because he thought he was able 
to write a licence and the resulting text is both undecipherable and 

- many programs, since they come from different origins, have the same 
name. At least three "scan" executables to put in /usr/bin, besides MH's 
scan. Should I create a /usr/gensoft tree, like we do here to prevent 
name clashes? (Yes, I know only X11 does that on Debian, but the set of 
all biology programs is almost as large.)

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

May be I could draw experience from the people who package other 
scientific sets, but there seems to be very few domain-specific programs 
in Debian?

Molecular Linux

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