[ensembl-dev] ENSEMBL INSTALLATION ISSUE: Regulation AJAX error

Beth Yates bp1 at sanger.ac.uk
Fri Feb 22 12:31:49 GMT 2013


Hi Rafael,

We have changed the way in which you set the path to these files, the 
variable you now need to set is DATAFILE_BASE_PATH and this should be 
set in SiteDefs.pm. The instructions for setting up these files for use 
are in the README file on the ftp site where you would have downloaded 
the files from.

ftp://ftp.ensembl.org/pub/current_data_files/homo_sapiens/GRCh37/result_feature/README

Hope this helps,
Beth

On 22/02/13 12:18, Rafael Hernández wrote:
> Hi,
>
> I've installed a local version of Ensembl release 70 following the 
> provided documentation and everything works fine except the Regulation 
> tools (example 
> <http://www.ensembl.org/Homo_sapiens/Regulation/Cell_line?db=funcgen;fdb=funcgen;r=17:46617590-46621119;rf=ENSR00001348194> of 
> regulation tool).
> When I query Ensembl looking for regulation info, it produces an AJAX 
> error and no graphics are showed.
> Below the error message:
>
> *AJAX error - Runtime Error in component 
> EnsEMBL::Web::Component::Regulation::FeaturesByCellLine [content]"*
> Function EnsEMBL::Web::Component::Regulation::FeaturesByCellLine fails 
> to execute due to the following error:
>
> -------------------- EXCEPTION --------------------
> MSG: Failed to open:
> ... 
> /result_feature/GM12878_DNase1_ENCODE_Uw/result_features.GM12878_DNase1_ENCODE_Uw.130.col
> No such file or directory
>
>
> I know the cause of the problem: Ensembl tries to read some files from 
> a directory located in the root of the file system  (e.g. 
>  /result_feature/GM12878_DNase1_ENCODE_Uw/result_features.GM12878_DNase1_ENCODE_Uw.130.col), 
> however the directory /result_feature/ doesn't exists and the query 
> crashes.
>
> If I move the /result_feature/ folder to the root of my file system, 
> then Ensembl works, however I don't want to put there those files, and 
> I want to know how could I change this. I found in the ensembl-dev 
> page a thread talking about this problem (here 
> <http://lists.ensembl.org/pipermail/dev/2012-April/007279.html>) and 
> they suggested to set a variable ENSEMBL_REGULATION_FILE_PATH pointing 
> to the desired folder in the DEFAULT.ini file.
> In my case should look like this:
>
> ENSEMBL_REGULATION_FILE_PATH=/usr/local/ensembl/regulation_files/
>
> However it doesn't works. Nothing change when using this setting and 
> Ensembl still looking for the files in the previous directory. Any idea?
>
> Thank you and best regards,
>
>
> Rafa Hernández de Diego
>
>
>
>
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