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Re: Biology packages in FreeBSD

On Tue, 24 May 2005, Nelson A. de Oliveira wrote:

[Sorry for splitting this up into more than one mail ... I should have read
 until the end
 So here I continue the quotes of William R. Pearson <wrp@virginia.edu>]

[EMAIL 2]:

It did not occur to me that you would only want to distribute binaries,
since they are not very useful without DNA and/or protein sequence databases
(which are considerably larger).  Are you planning on a distribution
that includes sequence databases?
There were discussions in the past to provide also data in a seperate
area of the Debian mirrors.  But there was no final decision and more
importantly nobody who did something about it.

I can certainly see an advantage to a
distribution that has pre-compiled versions of the programs (possibly pre-configured
to recognize the databases).
I would regard it as a remarkable enhancement to add some scripts to the
precompiled packages which download databases, put them in a defined location
and do the necessary configuration to work on these databases.

Are you basically talking about databases which are available at

     ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/data/  ?

Would you consider it reasonable to include one of these databases as
a working example?

IMHO this makes the real quality of a Debian package to provide this kind
of extra support for our users.  If you ask me a Debian developer is the
missing link between the developer (you) and the user.
Do you think that a download and compile script can fullfill this position?


I do not think there is much reason to distribute only my program,
because compiling my program is the smallest of the several steps required to
having a working FASTA system.
This is true for many programs - but I personally hate it anyway. Having
to do many even simple steps is boring compared to do only one single step
and beeing read.

Downloading the databases and editing
configuration files to find the databases is much more time consuming
and confusing.
So our part would be to reduce this hardness and confusion by providing
some reasonable documentation at the place where users expect it
(/usr/share/doc/fasta) and writing scripts which simplify the configuration -
at least this is my vision about Debian and especially Debian-Med.

So, I would prefer that FASTA not be included in your distribution,
though I encourage you to include a script that would allow people to
download and compile FASTA.
Well, we would respect your wish here and because you did not put an
explicite license to your software (which you should IMHO in any case
for instance stating exactly your opinion you mentioned above) we are
not able to provide it.  On the other hand you might consider the advantages
of Free Software.  Imagine that some people just learn about fasta because
it is provided with Debian and start sending you useful patches.


"your distribution" = Debian

So, I think that fasta is out of Debian, right?
Well, lets wait for a further answer.  Thanks Nelson for doing this
conversation and thanks again to William for his thoughts and providing

Kind regards



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