Dear Galaxy

Recently grooming has taken a few days. Is this typical?


Scott Tighe
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
University of Vermont
Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
802-656-2557

On 8/7/2013 3:37 AM, Fabrice BESNARD wrote:
Hi,

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 :
http://sourceforge.net/projects/snpeff/files/databases/v3_3/).
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,


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