Hello Scott, The public Main Galaxy instance at https://main.g2.bx.psu.edu (http://usegalaxy.org) is busy. It was even busier earlier in the week. Queuing jobs sequentially and/or running workflows is a great strategy to make sure that your jobs are in the queue when a processing window opens up. We know that varying delays can seem unpredictable, but have tried to clarify how job processing works in this wiki: http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute Take care, Jen Galaxy team On 8/8/13 6:18 AM, Scott Tighe wrote:
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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