Using SnpEff in the Galaxy main server, I need the Caenorhabditis briggsae
genome as a reference, which is not an option in the genome list given by
the tool as implemented in Galaxy right now.

In the doc of SnpEff, it is said that this database is available
(c_briggsae_WS230, down-load link here :
However, the version of SnpEff in Galaxy is 1.0. It is said in the SnpEff
docs that the database version should match the SnpEff version
(http://snpeff.sourceforge.net/download.html). I found that the first
release of a C. briggsae database dates back to the version 2.1 of SnpEff
(See here: http://sourceforge.net/projects/snpeff/files/databases/v2_1/).

Would it be to possible to up-date the list of databases of SnpEff in the
main server, to include the C. briggsae WS230?
If versions are not compatible, would it be possible to update SnpEff to a
more recent version?

If this is not possible right now (I  must confess I don't know how much
work this upddate would require), I guess the best and quickest
alternative option would be to install a SnpEff locally. Do you think it's
worth trying this, knowing that I don't feel very comfortable with
informatics (In other words, is the installation easy) ?

many thanks in advance for your comments and advices,

Fabrice Besnard
Institute of Biology of the Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75230 Paris cedex 05, France
8th floor. Office: Room 802. Lab: Room 817.
mail: fbesn...@biologie.ens.fr
Tel: +33-1-44-32-39-44

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to