SUMMARY: Intent to package: molecular biology programs
On Friday 28 August 1998, at 15 h 17, the keyboard of Stephane Bortzmeyer
<bortzmeyer@pasteur.fr> wrote:
> I'm thinking about packaging for Debian several molecular biology
> programs.
It seems there is interest to do so, I've already packaged ClustalW and
Phylip to get an idea, I'm working on it...
Any idea of the level of interest necessary to get a Biology section like
there is a Mathematics section? In the mean time, I'll send them to Misc.
> - 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?
For the coding, I can do nothing (too much to do, so little to live), for
the man page, I'll use undocumented(7) and try to translate the
documentation in nroff if I have time. (The licences can be a problem.)
> - 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
> retentive.
Calling my lawyer... I plan a long time to read the licence, write polite
letters to the author, waiting the reply, etc.
> - 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.)
Problem not solved, apparently. (See the thread "name clashes".) The
wrapper for Phylip could be a solution for such a "many binaries" package.
> - 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?
Blast, for instance, which we use here against humongous databases like Genbank, seems to be used also with local banks which are much smaller.
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