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Re: Packaging EMBOSS and data for EMBOSS

On Sat, 28 Apr 2007, Charles Plessy wrote:

- Indexes an EMBL-formatted miRNA database for EMBOSS, ships it in
  /usr/share/mirbase/emboss (should the database itself be
  /usr/share/mirbase/embl ?), and drops a small embossrc file in
- converts it to FASTA format using EMBOSS, and ships it in
  /usr/share/mirbase (/usr/share/mirbase/fasta ?)
- Indexes it for NCBI-Blast with formatdb, and ships it in
- will later insall the mirbase as a mySQL database.

Do you think that the layout makes sense? EMBOSS can tap in databases in
various directories, and I was thinking that users can make symlinks
from /usr/share/mirbase/blast/mir* to the directory to which BLASTDB

Well, a "database" sounds like something that changes frequently.  So
the right location would be /var/lib/mirbase.  Or is it rather a static
file once it was installed?  If it is static I have no problems with
your /usr/share suggestion.  If not do a "s?/usr/share?/var/lib?" to
your suggestion.

Also, mirbase is quite small, and I am wondering when it would make
sense to split that kind of package between mirbase-blast, mirbase-fasta
and mirbase-embl for instance.

Well, I'm *personally* in favour of splitting into reasonable modules
regarding functionality.  But there is no good rule and thus I would
advise you according your own preference.

I think that with a size of ~ 3 Mo it is intersting to provide mirbase
from within Debian, but definitely this scheme is not valid for bigger
sizes. The human genome is definitely to be packaged as a wrapper, but
where to put the cutoff?

Well, this might trigger the discussion about a data repository for Debian
that pops up every six months on debian-devel mailing list.

Lastly, as all of this takes some space, I also wonder if it is
acceptable by policy to have the heavy data under something like
/usr/share/bioinformatics, in order to let sysadmins dedicate a
partition to this.

This proposal makes some sense but I would suggest to discuss this
on debian-devel.

Kind regards



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