Re: Intent to package: molecular biology programs
On Fri, Aug 28, 1998 at 03:17:32PM +0200, Stephane Bortzmeyer wrote:
>
> [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?
No that is no reason to put them in contrib.
There are plenty of programs in debian which are horrendously coded :)
No man page is technically a bug (man pages aren't hard to write)
> - 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.
Then if the licence doesn't meet DSFG guidlines it must go in
non-free...unless you can maybe contact the authors and politely
ask them to change their licenses...who knows? maybe?
(if they are making money off them then chances are your out of luck)
> - 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.)
Well....
That would violate the FHS. According to the FSSTND and The FHS NO PACKAGE
may make a directory off of /usr excpet the ones listed in the standard.
Things should be properly broken up.
X11 does this because the standard allows it...It also (AFAIR) says that
allowing X11 to do this is only because of tradition AND that X11 is
kinda big and it would be a major PITA to change that.
> - 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?
I don't...but I work fixing Macs and Win95 machine for Mass General Hospital
in the CNY campus (research end) ...lots of Biology (and specifically medical)
research going on around me. Lots of posters with pictures, which I (from my
limited Biology classes in High School) identify as output from
those high voltage electrophoresus (sp?) machines to determine
sequences of nucleotides in DNA plastered up and down the hallways.
something specific you are looking for? :) I could ask around :)
-Steve
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