Hello,<br><br>I've been trying to set up a MOD website using GMODWeb, using the reccomended method of CENTOS4 and the RPMs available through <a href="http://biopackages.net" target="_blank">biopackages.net</a>, 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. <br>
<br>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. <br>
<br>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. <br>
<br><br>Thank You For Your Time,<br>Chris Childers<br><br><br><br>The command I used to invoke turnkey_generate is as follows:<br><br><span style="font-family: courier new,monospace;">turnkey_generate --use_web_caching=0 --search_engine=lucene --output_type=web_mod_perl --dbuser=postgres --dbpass= --dbhost=localhost --wwwemail=admin@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</span><br style="font-family: courier new,monospace;">
<br>Resulting in this output:<br><br><br><span style="font-family: courier new,monospace;">+------------------------------------------------------------------+</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">| TURNKEY INSTALLATION HELP |</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">+------------------------------------------------------------------+</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">perl turnkey_generate</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">If the file "build.conf" can be found from a previous run of the</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">turnkey_generate, you will be prompted to confirm the values saved in</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">this file. Please set your TURNKEY_ROOT environment variable before</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">running this script. Arguments can be provided on the command</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">line (such as --dbhost=foo), interactively, or with a build.conf file.</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Building with the following options:\nINSTALL_PATH /var/www/Sce2/S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">PACKAGE</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">SEARCH_ENGINE lucene</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">DEMO gmod-web-Sce</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">WWWEMAIL admin@host</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">OUTPUT_TYPE web_mod_perl</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">DBNAME chado-Sce-S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">SQLFILE_PATH /var/lib/gmod/src/chado/modules/default_nofuncs.sql</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">CONCAT Sce2S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">WWWHOST localhost</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">JDBC_DRIVER_STR</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">USE_WEB_CACHING 0</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">SKIP_TABLES affymetrixprobeset,affymetrixprobe,affymetrixcel,affymetrixsnp,affymetrixmas5,affymetrixdchip,affymetrixvsn,affymetrixsea,affymetrixplier,affymetrixdabg,affymetrixrma,affymetrixgcrma,affymetrixprobesetstat</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">SQLFAIRY_PATH /usr/bin/sqlt</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">DBHOST localhost</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">DBUSER postgres</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">USEDEMO 1</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">OUTPUT_PATH /tmp/var/www/Sce2/S228C</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">DBPORT 5432</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">WWWPORT 80</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">DBPASS</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">VIRTUAL N</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">URI_PREFIX Sce2/S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">JDBC_CONNECTION_STR</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">HIBERNATE_SQL_DIALECT</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Building with the following options:</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> DBHOST = localhost</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> DBPORT = 5432</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> VIRTUAL = N</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> WWWHOST = localhost</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> WWWPORT = 80</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> WWWEMAIL = admin@host</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> DBNAME = chado-Sce-S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> DBUSER = postgres</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> DBPASS =</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> OUTPUT_PATH = /tmp/var/www/Sce2/S228C</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> INSTALL_PATH = /var/www/Sce2/S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> SQLFILE_PATH = /var/lib/gmod/src/chado/modules/default_nofuncs.sql</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> SKIP_TABLES = affymetrixprobeset,affymetrixprobe,affymetrixcel,affymetrixsnp,affymetrixmas5,affymetrixdchip,affymetrixvsn,affymetrixsea,affymetrixplier,affymetrixdabg,affymetrixrma,affymetrixgcrma,affymetrixprobesetstat</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> SQLFAIRY_PATH = /usr/bin/sqlt</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> CONCAT = Sce2S228C</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> URI_PREFIX = Sce2/S228C</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> USEDEMO = 1</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> DEMO = gmod-web-Sce</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Parsing schema in '/var/lib/gmod/src/chado/modules/default_nofuncs.sql'...Conf file: /var/lib/gmod/src/chado/modules/default_nofuncs.sql</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Installing log4perl.conf in /tmp/var/www/Sce2/S228C/conf...</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Generating Turnkey...</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Creating directories...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Copying Turnkey framework files to '/tmp/var/www/Sce2/S228C'...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making soap settings file...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making httpd files...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making XML configuration file...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making object/relational Model classes...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making Atom display classes...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making default Atom display classes...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making default Search settings file...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making default header file...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making edit file...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making default Atom display templates...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">Argument "" isn't numeric in subtraction (-) at /usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2 line 2.</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Argument "" isn't numeric in subtraction (-) at /usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2 line 2.</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Argument "" isn't numeric in addition (+) at /usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2 line 8.</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Argument "" isn't numeric in addition (+) at /usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2 line 8.</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">Argument "" isn't numeric in numeric lt (<) at /usr/share/doc/turnkey-1.3/tt2/default/includes/hit_links.tt2 line 8.</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making search plugin template...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making root Turnkey object...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making default ini file...done!</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;"> +Making default index.html file...done!</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;"> +Making customized demo files...done!</span><br style="font-family: courier new,monospace;"><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">+------------------------------------------------------------------+</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">| Turnkey installation is complete. Now, add a line like:</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">|</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">| Include /var/www/Sce2/S228C/conf/httpd.conf</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">|</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">| to your base httpd.conf file, and restart Apache.</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">+------------------------------------------------------------------+</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><br>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 <a href="http://localhost/Sce2/S228C/" target="_blank">http://localhost/Sce2/S228C/</a><br>
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:<br><br><br><span style="font-family: courier new,monospace;">[Mon Mar 17 15:34:55 2008] [error] [client <a href="http://127.0.0.1" target="_blank">127.0.0.1</a>] 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</span><br>
<br>