[ensembl-dev] Help with Ensembl installation

Ernesto Benedito ebenedito at appzero.com
Tue May 10 14:49:18 BST 2011


Just an update that this is now working for me (at least apache is
starting)

Yesterday I had some time to follow up the Perl scripts and the problem
was with that ENSEMBL_CUSTOMLOG not being defined in SiteDefs.pm..   I
don't recall any mention about this in the documentation :-(  

Also, the docs didn't mention apache being built with -enable-headers
and -enable-expires..   There were other things I had to do to get it up
and running to this point.   Anyway, each mileage varies. 

Below is what I get now.. Thanks for all the help.. 
Regards

-----------------------
 [root at appzensembl ~]# /start

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://appzensembl.trigence.com:80

 Cache namespace:    http://appzensembl.trigence.com

 Server root:        /usr/local/ensembl

 PID file:           /usr/local/ensembl/logs/pid_file
 Access logs:        /usr/local/ensembl/logs/custom_log combined
 Error logs:         /usr/local/ensembl/logs/error_log

 CSS file:
http://appzensembl.trigence.com/minified/c40cb4cf7a0e00d5dcc1e4c4c6ba90a
a.css
 JavaScript file:
http://appzensembl.trigence.com/minified/eba083030693b7669127f3ff3ba6db7
5.js

 Plugins installed:  EnsEMBL::Mirror
                     EnsEMBL::Ensembl
                     

========================================================================
======

ENSEMBL_BLAST_METHODS config unavailable at
/usr/local/ensembl/modules/EnsEMBL/Web/BlastView/BlastDefs.pm line 66.
[root at appzensembl ~]#

-----Original Message-----
From: Ernesto Benedito 
Sent: Monday, May 09, 2011 1:55 PM
To: 'William Spooner'
Cc: dev at ensembl.org
Subject: RE: [ensembl-dev] Help with Ensembl installation

Hi William,
Thanks for your quick reply.. It is much appreciated.

I have the following test script:

	#!/usr/bin/perl

	use Net::Domain qw(hostname hostfqdn hostdomain);
  
	my $host = hostname();
	print "The host name is $host \n";

and I get the proper "The host name is appzensembl"... 

Also, when calling for "hostname" in the command shell, it returns the
proper hostname as well (which is hardcoded in /etc/host and
/etc/nsswitch.conf). 

However, the clue you have provided me could lead me to something.. I
will continue playing with it (tracing it with strace) to see if I find
out more. 

Regards,

-----Original Message-----
From: William Spooner [mailto:whs at eaglegenomics.com] 
Sent: Monday, May 09, 2011 1:25 PM
To: Ernesto Benedito
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] Help with Ensembl installation

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/c40cb4cf7a0e00d5dcc1e4c4c6ba90a
a.css
>  JavaScript file:
http://appzensembl.trigence.com/minified/eba083030693b7669127f3ff3ba6db7
5.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




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