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Re: Packaging EMBOSS and data for EMBOSS

Le Sat, Apr 28, 2007 at 07:27:44PM +0200, Steffen Moeller a écrit :
> On Saturday 28 April 2007 15:56:40 Andreas Tille wrote:
> > On Sat, 28 Apr 2007, Charles Plessy wrote:
> [...]
> > > 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.
> One of the many projects I once started is a script to download the databases 
> for me. Hence, much like the MS fonts, the script should be in Debian but the 
> data not. We'd end up with well-described paths for the data but would not 
> spam Debian with too many large packages.
> With respect to the suggested subfolder I think that this should be come a 
> paramter of the script. /var/lib for those with recently bought computers 
> from the local discounter and tons of disk space working at home, those with 
> a network wil decide for something shared.

Hi Andreas and Steffen,

For the particular case of mirbase, there is a release every quarter
aproximately. I think that it makes it suitable for being directly
packaged, and in therory, the data should go to /usr/share as it is
shareable and static.

But on the other hand, if the idea of having a common folder of sequence
databases is accepted, it would be a bit stupid to keep small databases
in /usr/share for the sake of it, separtating them from big genomes
which would go in /var/somewhere. But the problem is that there is no
/var/share, although it could be cool to have a nfs- or samba-mountable
folder in local networks, from which people using modern OSes could
access the data when they do not need a dedicated server to run the

Alternatively, and similarly to java-package, we could have
some wrappers which would produce .deb pacakges from freshly downloaded
genomes. In that case /usr/share/genomics-or-whatever would be a good
target again.

Lastly, if we make enough progressees, maybe we can try to re-contact
Bill Pearson and ask him if he reconsiders his decision about not
distributing FASTA in Debian...


Have a nice day,

Charles Plessy
Wako, Saitama, Japan

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