[Gmod-help] I am having trouble setting up a MOD website using Turnkey/GMODWeb
Chris Childers
genetics.guy at gmail.com
Mon Mar 17 15:47:33 EDT 2008
Hello,
I've been trying to set up a MOD website using GMODWeb, using the
reccomended method of CENTOS4 and the RPMs available through biopackages.net,
with mixed success. The MOD website included in the install (Aliased to
localhost/GmodWeb)generates a "500 Internal Server Error", while the two
sample databases and sites seem to install and load just fine. I then tried
making a MOD website for one of our Chado databases, hosted on another
server (with no success). I was not certain about being able to access a
remote database in this way, so I decided to try something simpler: to
recreate one of the existing MOD sites that I had installed via RPM.
I attempted to create a second Sce database website by taking the sample
turnkey generate statement from the website and supplementing that with
information I was able to glean from the turnkey_generate code and the "
gmod-web.spec" file in "gmod-web-1.3-1.29.bp.centos4.src.rpm" (I am pretty
sure that was the rpm that installs the Sce demo site). I then added the
suggested line to the base httpd.conf file, and this also resulted in a 500
Internal Server Error. I have tried modifying different settings and
locations in the hopes that something simple was set incorrectly, but
nothing I have tried has worked.
I apologize for including so much text below, but I though it would be
better if I included more information instead of less. I have been trying to
work through this for some time now, and wanted to exhaust all of my ideas
before bothering you guys. Any suggestions, tips or advice you might have
would be greatly appreciated.
Thank You For Your Time,
Chris Childers
The command I used to invoke turnkey_generate is as follows:
turnkey_generate --use_web_caching=0 --search_engine=lucene
--output_type=web_mod_perl --dbuser=postgres --dbpass= --dbhost=localhost
--wwwemail=admin at host--sqlfile_path=/var/lib/gmod/src/chado/modules/default_nofuncs.sql
--skip_tables=affymetrixprobeset,affymetrixprobe,affymetrixcel,affymetrixsnp,affymetrixmas5,affymetrixdchip,affymetrixvsn,affymetrixsea,affymetrixplier,affymetrixdabg,affymetrixrma,affymetrixgcrma,affymetrixprobesetstat
--dbname=chado-Sce-S228C --output_path=/tmp/var/www/Sce2/S228C
--install_path=/var/www/Sce2/S228C --dbport=5432 --concat=Sce2S228C
--uri_prefix=Sce2/S228C --virtual=N --wwwport=80 --wwwhost=localhost
--usedemo=1 --demo=gmod-web-Sce --sqlfairy_path=/usr/bin/sqlt
Resulting in this output:
+------------------------------------------------------------------+
| TURNKEY INSTALLATION HELP |
+------------------------------------------------------------------+
perl turnkey_generate
If the file "build.conf" can be found from a previous run of the
turnkey_generate, you will be prompted to confirm the values saved in
this file. Please set your TURNKEY_ROOT environment variable before
running this script. Arguments can be provided on the command
line (such as --dbhost=foo), interactively, or with a build.conf file.
Building with the following options:\nINSTALL_PATH /var/www/Sce2/S228C
PACKAGE
SEARCH_ENGINE lucene
DEMO gmod-web-Sce
WWWEMAIL admin at host
OUTPUT_TYPE web_mod_perl
DBNAME chado-Sce-S228C
SQLFILE_PATH /var/lib/gmod/src/chado/modules/default_nofuncs.sql
CONCAT Sce2S228C
WWWHOST localhost
JDBC_DRIVER_STR
USE_WEB_CACHING 0
SKIP_TABLES
affymetrixprobeset,affymetrixprobe,affymetrixcel,affymetrixsnp,affymetrixmas5,affymetrixdchip,affymetrixvsn,affymetrixsea,affymetrixplier,affymetrixdabg,affymetrixrma,affymetrixgcrma,affymetrixprobesetstat
SQLFAIRY_PATH /usr/bin/sqlt
DBHOST localhost
DBUSER postgres
USEDEMO 1
OUTPUT_PATH /tmp/var/www/Sce2/S228C
DBPORT 5432
WWWPORT 80
DBPASS
VIRTUAL N
URI_PREFIX Sce2/S228C
JDBC_CONNECTION_STR
HIBERNATE_SQL_DIALECT
Building with the following options:
DBHOST = localhost
DBPORT = 5432
VIRTUAL = N
WWWHOST = localhost
WWWPORT = 80
WWWEMAIL = admin at host
DBNAME = chado-Sce-S228C
DBUSER = postgres
DBPASS =
OUTPUT_PATH = /tmp/var/www/Sce2/S228C
INSTALL_PATH = /var/www/Sce2/S228C
SQLFILE_PATH = /var/lib/gmod/src/chado/modules/default_nofuncs.sql
SKIP_TABLES =
affymetrixprobeset,affymetrixprobe,affymetrixcel,affymetrixsnp,affymetrixmas5,affymetrixdchip,affymetrixvsn,affymetrixsea,affymetrixplier,affymetrixdabg,affymetrixrma,affymetrixgcrma,affymetrixprobesetstat
SQLFAIRY_PATH = /usr/bin/sqlt
CONCAT = Sce2S228C
URI_PREFIX = Sce2/S228C
USEDEMO = 1
DEMO = gmod-web-Sce
Parsing schema in
'/var/lib/gmod/src/chado/modules/default_nofuncs.sql'...Conf file:
/var/lib/gmod/src/chado/modules/default_nofuncs.sql
done!
Installing log4perl.conf in /tmp/var/www/Sce2/S228C/conf...
Generating Turnkey...
+Creating directories...done!
+Copying Turnkey framework files to '/tmp/var/www/Sce2/S228C'...done!
+Making soap settings file...done!
+Making httpd files...done!
+Making XML configuration file...done!
+Making object/relational Model classes...done!
+Making Atom display classes...done!
+Making default Atom display classes...done!
+Making default Search settings file...done!
+Making default header file...done!
+Making edit file...done!
+Making default Atom display templates...done!
Argument "" isn't numeric in subtraction (-) at
/usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2
line 2.
Argument "" isn't numeric in subtraction (-) at
/usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2
line 2.
Argument "" isn't numeric in addition (+) at
/usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2
line 8.
Argument "" isn't numeric in addition (+) at
/usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2
line 8.
Argument "" isn't numeric in numeric lt (<) at
/usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2
line 8.
+Making search plugin template...done!
+Making root Turnkey object...done!
+Making default ini file...done!
+Making default index.html file...done!
+Making customized demo files...done!
+------------------------------------------------------------------+
| Turnkey installation is complete. Now, add a line like:
|
| Include /var/www/Sce2/S228C/conf/httpd.conf
|
| to your base httpd.conf file, and restart Apache.
+------------------------------------------------------------------+
I included this line in my base httpd.conf file, below the other lines
generated by the rpm installs, then restarted Apache, and browsed over to
http://localhost/Sce2/S228C/
This also causes Apache to throw out 500 errors, and after culling the log
files, I saw the following in /etc/httpd/logs/error_log:
[Mon Mar 17 15:34:55 2008] [error] [client 127.0.0.1]
TurnkeySce2S228C::Request _init_dbobject() failed at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Root.pm line
83\n\tTurnkeySce2S228C::Root::die('TurnkeySce2S228C::Request=HASH(0xdc1c528)',
'TurnkeySce2S228C::Request _init_dbobject() failed') called at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Request.pm line
218\n\tTurnkeySce2S228C::Request::init('TurnkeySce2S228C::Request=HASH(0xdc1c528)',
'r', 'Apache::ParseFormData=SCALAR(0xdc1c660)') called at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Request.pm line
153\n\tTurnkeySce2S228C::Request::new('TurnkeySce2S228C::Request', 'r',
'Apache::ParseFormData=SCALAR(0xdc1c660)') called at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Render.pm line
75\n\tTurnkeySce2S228C::Render::handler('Apache::ParseFormData=SCALAR(0xdc1c660)')
called at -e line 0\n\teval {...} called at -e line 0\n
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