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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--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
