The version of SnpEff on the public Main Galaxy server is "2.1a (build
2012-04-20)". (The wrapper version is 1.0).
The wrapper may or may not be appropriate for the newer version, I
wasn't able to find that in the documentation. The tool/wrapper author
can be contacted if you want to ask. Log into the tool shed to find
contact information or contact through the SnpEff web site (probably better)
: tool is named "snpeff" and the author is
There are no immediate plans to update Main, but this could change. If
you wanted to submit an enhancement request, please see:
The best current way to use the tool with this genome is with a local or
cloud instance and a matched wrapper (as confirmed by the tool author).
On 8/7/13 12:37 AM, Fabrice BESNARD wrote:
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
). 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,