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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hello everyone,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I would like to install an Ensembl website/app for testing..
I have questions regarding an application dependency error (Blast) that I am
getting..<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><u><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Background: <o:p></o:p></span></font></u></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- Platform is a RedHat 5.4 server 64 bits<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- I would like to achieve a minimum installation of Ensembl without
having to download the 600GB of available databases.. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- 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. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- 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) <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- I am using release-62, and downloaded the following
databases:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>-<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>ensembl_website_62<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>-<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>ensembl_production_62<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>-<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Saccharomyces_cerevisiae <o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>-<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'>
</span></font></span></span></font><![endif]><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>and have created the “ensemble_web_user_db”<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I picked Saccharomyces_cerevisiae as the species as it is
the smallest DB I could find from the DB repository<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><This is the output of what I get when stating apache:><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'>[root@appzensembl ensembl]#
/usr/local/ensembl/apache2/bin/httpd –d /usr/local/ensembl<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Starting up Ensembl server on host:
appzensembl<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Executing perl startup file<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Retrieving conf from
/usr/local/ensembl/conf/config.packed<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>unknown database type
DATABASE_PRODUCTION<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>unknown database type
DATABASE_PRODUCTION<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>==============================================================================<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Server information:<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>==============================================================================<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Ensembl version: 62<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> External address:
http://appzensembl.trigence.com/<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Real address: http://This
account is currently not available.:80<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> </span></font><font size=2
face=Arial><span lang=FR style='font-size:10.0pt;font-family:Arial'>Cache
namespace: http://appzensembl.trigence.com<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'> </span></font><font size=2
face=Arial><span style='font-size:10.0pt;font-family:Arial'>Server root:
/usr/local/ensembl<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> PID file: /usr/local/ensembl/logs/This
account is currently not available..httpd.pid<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Access logs:
/usr/local/ensembl/logs/This account is currently not available..access_log
ensembl_extended<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> Error logs:
/usr/local/ensembl/logs/This account is currently not available..error_log<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> CSS file:
http://appzensembl.trigence.com/minified/c40cb4cf7a0e00d5dcc1e4c4c6ba90aa.css<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> </span></font><font size=2
face=Arial><span lang=FR style='font-size:10.0pt;font-family:Arial'>JavaScript
file:
http://appzensembl.trigence.com/minified/eba083030693b7669127f3ff3ba6db75.js<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'> Plugins installed:
EnsEMBL::Mirror<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'> EnsEMBL::Ensembl<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
lang=FR style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>==============================================================================<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>ENSEMBL_BLAST_METHODS config
unavailable at /usr/local/ensembl/modules/EnsEMBL/Web/BlastView/BlastDefs.pm
line 66.<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Syntax error on line 36 of
/usr/local/ensembl/conf/httpd.conf:<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>$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<o:p></o:p></span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>[root@appzensembl ensembl]#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><My questions are:><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- the app seems to be looking for something related to BLAST
and BlastView (as seen above)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- 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?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>- When I check the documentation on </span></font><strong><b><font
face="Times New Roman">the BioPerl modules</font></b></strong>, there is the following
warning related BLAST and BlastView:<o:p></o:p></p>
<p class=space-below style='margin-left:.5in'><strong><b><i><font size=3
face="Times New Roman"><span style='font-size:12.0pt;font-style:italic'>“Important
note</span></font></i></b></strong><i><span style='font-style:italic'>: Recent
versions of BioPerl are compatible with the Ensembl API but </span></i><em><i><font
face="Times New Roman"><span style='font-style:normal'>not</span></font></i></em><i><span
style='font-style:italic'> with the current, rather old, blastview code.<o:p></o:p></span></i></p>
<p class=space-below style='margin-left:.5in'><i><font size=3
face="Times New Roman"><span style='font-size:12.0pt;font-style:italic'>If you
wish to install BLAST/BLAT on your mirror site, you will need to find a copy of
BioPerl <strong><b><font face="Times New Roman">version 1.2.3</font></b></strong>
(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.<o:p></o:p></span></font></i></p>
<p style='margin-left:.5in'><i><font size=3 face="Times New Roman"><span
style='font-size:12.0pt;font-style:italic'>We are aiming to resolve this issue
in the not-too-distant future, by rewriting the Ensembl BLAST interface and
parse”<o:p></o:p></span></font></i></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>From that, I can infer that BioPerl <u>should</u> be
compatible with the current Ensembl API, cool, but if so, where are that
BLAST/BlastView dependencies coming from?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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..<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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!! <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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 <u>very,
very, very</u> minimal installation of Ensembl.. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks in advance<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>p.s. The end goal is to encapsulate this app using
application virtualization.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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