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,