[ensembl-dev] Help with Ensembl installation

[William Spooner]

Hi Ernesto,

You seem to be writing the access logs to a file called;

"/usr/local/ensembl/logs/This account is currently not available..access_log ensembl_extended"

I think that this filename, when passed to the mod-perl add_config method, is causing the fatal error (the others are 'just' warnings).

I also suspect that the root cause is your perl 'hostname()' function returning 'This account is currently not available'.

Best,

Will

On 9 May 2011, at 17:27, Ernesto Benedito wrote:

> Hello everyone,
>  
> I would like to install an Ensembl website/app for testing.. I have questions regarding an application dependency error  (Blast) that I am getting..
>  
> Background:
>  
> - Platform is a RedHat 5.4 server 64 bits
>  
> - I would like to achieve a minimum installation of Ensembl without having to download the 600GB of available databases..
>  
> - I am installing Ensembl for the first time and I have no background info on what this app (or the others; BioMart, BioPerl, etc) do.   
>  
> - I have installed all the prerequisites (apache, mysql, the 30 or more perl module dependencies) and downloaded the ensembl, biomart, bioperl code using CVS and also downloaded a few databases. I have created mysql users, added the DB tables, imported database data, etc..  BTW, during the initial installation process I had some issues related to prerequisites in my server (i.e.  libgd versions collision, expat-devel etc), and all that is gone now..  Apache starts, crawls through the initialization stages, but from what I can infer from the startup sequence, it is failing on a Ensembl application module dependency (see below)
>  
> - I am using release-62, and downloaded the following databases:
>  
> -          ensembl_website_62
> -          ensembl_production_62
> -          Saccharomyces_cerevisiae  
> -          and have created the “ensemble_web_user_db”
>  
> I picked Saccharomyces_cerevisiae as the species as it is the smallest DB I could find from the DB repository
>  
>  
> <This is the output of what I get when stating apache:>
>  
>  
> [root at appzensembl ensembl]# /usr/local/ensembl/apache2/bin/httpd –d /usr/local/ensembl
>  
> Starting up Ensembl server on host: appzensembl
>  Executing perl startup file
>  Retrieving conf from /usr/local/ensembl/conf/config.packed
> unknown database type DATABASE_PRODUCTION
> unknown database type DATABASE_PRODUCTION
>  
> ==============================================================================
>  Server information:
> ==============================================================================
>  
>  Ensembl version:    62
>  
>  External address:   http://appzensembl.trigence.com/
>  Real address:       http://This account is currently not available.:80
>  
>  Cache namespace:    http://appzensembl.trigence.com
>  
>  Server root:        /usr/local/ensembl
>  
>  PID file:           /usr/local/ensembl/logs/This account is currently not available..httpd.pid
>  Access logs:        /usr/local/ensembl/logs/This account is currently not available..access_log ensembl_extended
>  Error logs:         /usr/local/ensembl/logs/This account is currently not available..error_log
>  
>  CSS file:           http://appzensembl.trigence.com/minified/c40cb4cf7a0e00d5dcc1e4c4c6ba90aa.css
>  JavaScript file:    http://appzensembl.trigence.com/minified/eba083030693b7669127f3ff3ba6db75.js
>  
>  Plugins installed:  EnsEMBL::Mirror
>                      EnsEMBL::Ensembl
>                     
>  
> ==============================================================================
>  
> ENSEMBL_BLAST_METHODS config unavailable at /usr/local/ensembl/modules/EnsEMBL/Web/BlastView/BlastDefs.pm line 66.
> Syntax error on line 36 of /usr/local/ensembl/conf/httpd.conf:
> $parms->add_config() has failed: CustomLog takes two or three arguments, a file name, a custom log format string or format name, and an optional "env=" clause (see docs) at /usr/local/apache2/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Apache2/PerlSections.pm line 215.\n
> [root at appzensembl ensembl]#
>  
>  
>  
> <My questions are:>
>  
> - the app seems to be looking for something related to BLAST and BlastView (as seen above)
>  
> - Is the main problem of the start up sequence related to dependencies with BLAST (as seen at the end of the logs), or the DATABASE_PRODUCTION seen at the beginning?
>  
> - When I check the documentation on the BioPerl modules, there is the following warning related BLAST and BlastView:
> “Important note: Recent versions of BioPerl are compatible with the Ensembl API but not with the current, rather old, blastview code.
> 
> If you wish to install BLAST/BLAT on your mirror site, you will need to find a copy of BioPerl version 1.2.3 (unfortunately no longer available through the BioPerl CVS repository), not a more recent version. Starting with 1.2.4, major changes were made to the BioPerl API which make it incompatible with Ensembl blastview.
> 
> We are aiming to resolve this issue in the not-too-distant future, by rewriting the Ensembl BLAST interface and parse”
> 
> From that, I can infer that BioPerl should be compatible with the current Ensembl API, cool, but if so, where are that BLAST/BlastView dependencies coming from?
>  
> I am not familiar with the purpose of any of these apps (Ensembl, BioPerl, BLAST/BlastView)..  I just followed the docs on the Ensembl and the BioMart/BioPerl modules installation and now the app is complaining on these BLAST dependencies..
>  
> Is this something related to a configuration issue, a hard coded dependency in the Ensembl code that I downloaded from CVS, or simply because as the Ensembl app couldn’t figure out the DATABASE_PRODUCTION the app went on the wrong path?
>  
> If you can shed some light on how to tackle this start up issue before I start going through all the perl code to figure it out, it would be great!!
>  
> Also, if possible, a brief explanation on Ensembl and its dependencies it would be supper.  Remember that I am looking at this as a black box testing, not knowing much about these apps, and my purpose is to achieve a very, very, very minimal installation of Ensembl.. 
>  
> Thanks in advance
> p.s. The end goal is to encapsulate this app using application virtualization.
>  
>  
>  
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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com