[ensembl-dev] Help with Ensembl installation

Ernesto Benedito ebenedito at appzero.com
Mon May 9 17:27:57 BST 2011

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




- 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


- 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


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:

 JavaScript file:


 Plugins installed:  EnsEMBL::Mirror






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
/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


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




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