Re: GMAP -- Align mRNA and EST sequences to a genome

[Charles Plessy <plessy@debian.org>]

Hi Shaun,

here are extra comments en vrac:

Le Mon, May 10, 2010 at 05:31:12PM -0700, Shaun Jackman a écrit :
> >>
> >> The git repository is here:
> >> git://git.debian.org/git/debian-med/gmap.git
> >> http://git.debian.org/?p=debian-med/gmap.git

Please consider adding a ‘pristine-tar’ branch if it is easy for you.
http://wiki.debian.org/PackagingWithGit#pristine-tar

> How about /var/cache/gmap?
> http://www.pathname.com/fhs/pub/fhs-2.3.html#VARCACHEAPPLICATIONCACHEDATA

I think that /var/cache can be erased anytime by the administrator. Perhaps
/var/lib is more appropriate?

Also, we are discussing the possibility to distribute data packages. For
instance, we could distribute the human genome in FASTA format and indexed for
various software including gmap. In that case, it may be interesting to change
the default again to /usr/share/somewhere. The precise path has not been
seriously discussed yet (it will be probably better to keep all the distributed
data in the same tree, since it can require a large amount of disk space). You
can find more information in a recent thread on the debian-science discussion
list and on the Debian wiki:

http://lists.debian.org/msgid-search/20100508140545.GA19587@meiner
http://wiki.debian.org/DataPackages

> 
> I had changed the upstream version number from
> gmap-2010-03-09
> to
> gmap-20100309
> 
> This change isn't strictly necessary. Should I undo this?

I would recommend to use the same version number as Upstream when possible.

Have a nice day,

-- 
Charles