[ensembl-dev] Setting up an Ensembl Mirror

Will Spooner whs at eaglegenomics.com
Fri Oct 29 14:43:22 BST 2010

Hi Jonathan,

Sounds like a config problem. You need to make sure that your SiteDefs.pm has only the species for which you have installed databases. To debug, perhaps limit to just human? You will need to remove the conf/packed/* on server startup.


On 29 Oct 2010, at 09:45, <jonathan.churchill at stfc.ac.uk> <jonathan.churchill at stfc.ac.uk> wrote:

> Hello Everyone
> I wonder if anyone could help me with, what I'm sure is a simple configuration problem, of an Ensembl mirror site ?
> I have the mirror installed and running but I get errors when trying to display genes or transcripts. For example I get apache error log messages such as
> " No compara ENSEMBLGENE member for OTTHUMG00000017411 and compara "
> (from EnsEMBL/Web/Object/Gene.pm module)
> when trying to display a Gene, suggesting the compara database is missing (?) ie An empty string is returned for that DB.
> When trying to draw a transcript I get errors like
> "Can't call method "get" on an undefined value at ..../EnsEMBL/Web/Component/Transcript/TranscriptImage.pm line 32"
> Which again, looking at the code, I think implies that there is some object or database configuration missing. The 'Configuure this page' popup also only has the Sequence and Decorations tracks as options, missing the Genes, Preduiction transcripts, Variation Features etc. So this looks like a basic configuration error I've made somewhere.
> I have loaded all the human, rat, mouse and ensembl* databases from the ftp site and a number (but not all yet) of the other species. The mirror plugin has the basic items set in the SiteDefs.pm and minimum changes to Defaults.ini and a MULTI.ini that just contains
> [databases] 
> DATABASE_WEBSITE       = ensembl_website_59
> DATABASE_BLAST         = ensembl_blast
> DATABASE_COMPARA       = ensembl_compara_59
> Could anyone suggest some things I can take a look at or some ways of debugging the problem ?
> Many thanks
> Jonathan
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William Spooner
whs at eaglegenomics.com

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