[Gmod-help] I am having trouble setting up a MOD website using Turnkey/GMODWeb
Dave Clements, GMOD Help Desk
gmodhelp at googlemail.com
Mon Mar 17 16:16:22 EDT 2008
Chris,
I am forwarding your question on to the Turnkey mailing list, as
someone on that list may be able to answer your question.
Unfortunately, I have not yet worked with Turnkey/GMODWeb. There are
several known issues with Turnkey/GMODWeb and you may have hit one of
them.
Thank you for sending so much information. Often, we don't get enough.
Regards,
Dave Clements
GMOD Help Desk
On Mon, Mar 17, 2008 at 12:47 PM, Chris Childers <genetics.guy at gmail.com> wrote:
> 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
>
>
More information about the Gmod-help
mailing list