[Gmod-help] I am having trouble setting up a MOD website using Turnkey/GMODWeb
Chris Childers
genetics.guy at gmail.com
Tue Mar 18 08:28:40 EDT 2008
I just realized that the example I gave you was not the one I had intended
to. I had found that the install_path and output_path should be to the same
place. I still get the errors though. I am really sorry about causing any
confusion.
Thanks,
Chris
Here is the proper output:
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=/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
+------------------------------------------------------------------+
| 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 /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 = /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 /var/www/Sce2/S228C/conf...
Generating Turnkey...
+Creating directories...done!
+Copying Turnkey framework files to '/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.
+------------------------------------------------------------------+
the errorlog still shows this problem after I restart httpd and try looking
at where the site should be:
Not using cache for: /Sce2/S228C/db/index at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Render.pm line 72.
[Tue Mar 18 08:29:47 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(0xbf14ad0)',
'TurnkeySce2S228C::Request _init_dbobject() failed') called at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Request.pm line
218\n\tTurnkeySce2S228C::Request::init('TurnkeySce2S228C::Request=HASH(0xbf14ad0)',
'r', 'Apache::ParseFormData=SCALAR(0xaa95318)') called at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Request.pm line
153\n\tTurnkeySce2S228C::Request::new('TurnkeySce2S228C::Request', 'r',
'Apache::ParseFormData=SCALAR(0xaa95318)') called at
/var/www/Sce2/S228C/lib/TurnkeySce2S228C/Render.pm line
75\n\tTurnkeySce2S228C::Render::handler('Apache::ParseFormData=SCALAR(0xaa95318)')
called at -e line 0\n\teval {...} called at -e line 0\n
On Mon, Mar 17, 2008 at 4:16 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:
> 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
> >
> >
>
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