Database of c_briggsae_WS230 for SnpEff
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, -- 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: fbesnard@biologie.ens.fr Tel: +33-1-44-32-39-44
Hi Fabrice, 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) http://toolshed.g2.bx.psu.edu: tool is named "snpeff" and the author is "pcingola" http://snpeff.sourceforge.net/ There are no immediate plans to update Main, but this could change. If you wanted to submit an enhancement request, please see: http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board 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). http://getgalaxy.org http://usegalaxy.org Best, Jen Galaxy team On 8/7/13 12:37 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,
-- Jennifer Hillman-Jackson http://galaxyproject.org
participants (2)
-
Fabrice BESNARD -
Jennifer Jackson