Re: Packaging EMBOSS and data for EMBOSS
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.
Another issue I was addressing in this matter, which also helped to demotivate
my work on the above-scetched script, is the utilisation of local tools
combined with web-services in workflows as they are presented via Taverna
(taverna.sf.net). We'd thus need the data only at few redundant sites of the
internet. But, admittedly, this often works better in PowerPoint than in real
life.
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.
Cheers,
Steffen
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