Re: [mart-dev] errors when starting martview

Thu, 26 Nov 2009 08:34:52 -0800 

Hi Rui,
you need to find the apache processes in process list, say ps -ef and kill the apache process that you started. If you start apache from biomart-perl directory, the process id file httpd.pid should be under biomart-perl/logs 

Cheers
Syed


Jing, Rui wrote:

Hi Syed,

 
Here is screen copy after execute b.

I add the path for apxs in settings.conf:
apxs=/common/home/hge/software/biomart-perl/apache/bin/apxs

 
By the way, I can not stop martview by:

kill `cat logs/httpd.pid`
bash: kill: (19006) - No such process
what should I do?

 
[r...@node01 74]> perl bin/configure.pl -r conf/martDBLocation.xml --clean

Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
APACHE: /common/home/software/biomart-perl/apache/bin/httpd
HOST: localhost
PORT: 8011
PROXY:
LOCATION: biomart
APXS/2: /common/home/software/biomart-perl/apache/bin/apxs
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"

 
Got usable Apache in /common/home/software/biomart-perl/apache/bin/httpd,

probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl in
httpd.conf.
Libdir /common/home/software/biomart-perl/lib is not in @INC, adding to @INC
Connection parameters of [My BioMart Database]  [ OK ]

[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... My BioMart Database ...... 001/001 ... msd
....................................... (RDBMS) martdb.ebi.ac.uk:3306 .........
->  upgrading to 0.6/0.7 ...  OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/1] Attribute Panel of Dataset.. :msd
[1/1] Filter Panel of Dataset..... :msd


 
 
Thanks,
 
Ray


________________________________

From: Syed Haider [mailto:[email protected]]
Sent: Thu 11/26/2009 9:59 AM
To: Jing, Rui
Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
Subject: Re: [mart-dev] errors when starting martview





Jing, Rui wrote:

Hi Syed,

Here is screen copy after execute b.
by the way, I installed my local biomart into

/common/home/software/biomart-perl

(it is biomart-perl, do I need change settings.conf, LOCATION= biomart to
LOCATION=biomart-perl ?


no biomart is just fine, thats what becomes the part of your URL, its
not the location of biomart-perl on disk.

could you also add the path to apxs or apxs2 in setttings.conf and redo
the configure with --clean.

once done, please let us know if that works, also send us the screen
copy of terminal .

thanks
Syed



[r...@node01 50]> perl bin/configure.pl -r conf/martDBLocation.xml --clean
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
APACHE: /common/home/hge/software/biomart-perl/apache/bin/httpd
HOST: localhost
PORT: 8011
PROXY:
LOCATION: biomart
APXS/2:
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"

Got usable Apache in /common/home/software/biomart-perl/apache/bin/httpd,
probing for version & ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl

in

httpd.conf.
Libdir /common/home/software/biomart-perl/lib is not in @INC, adding to @INC
Connection parameters of [My BioMart Database]  [ OK ]

[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... My BioMart Database ...... 001/001 ... msd
....................................... (RDBMS) martdb.ebi.ac.uk:3306

.........

->  upgrading to 0.6/0.7 ...  OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/1] Attribute Panel of Dataset.. :msd
[1/1] Filter Panel of Dataset..... :msd

Thanks,

Ray

________________________________

From: Syed Haider [mailto:[email protected]]
Sent: Thu 11/26/2009 9:27 AM
To: Jing, Rui
Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
Subject: Re: [mart-dev] errors when starting martview



a- please set the location param in conf/settings.conf to
location=biomart

b- reconfigure the perl bin/configure.pl.... with --clean switch

c- kill and restart apache and  then access the URL as:
http://node01.com:8011/biomart/martview


please send us what see in terminal after executing 'b'

thanks
Syed




Jing, Rui wrote:

Hi Syed,

Great. It started.
Processing Cached Registry:


/common/home/software/biomart-perl/conf/cachedRegistries/martDBLocation.xml.cach

ed

cat logs/httpd.pid
19006

but when I visit hthttp://node01.com:8011/biomart-perl/martview
<http://node01.com:8011/biomart-perl/martview>
it gave error: Oops! This link appears to be broken from IE.

I used martDBLocation.xml
perl bin/configure.pl -r conf/martDBLocation.xml --clean

settings.conf is:
     5 apacheBinary=/common/home/software/biomart-perl/apache/bin/httpd
      6 serverHost=localhost
      7 port=8011
      8 # to use proxying set the proxy port below (even if its 80) and set
serverHost as your proxy host
      9 proxy=
     10 # if apxs or apxs2 is not in default directory where httpd lives, you
may set this param to point to apxs/2
     11 apxs=
     12 location=/common/home/software/biomart-perl
     13

 
please advise what the problem is.

Thanks,

Ray

________________________________

From: Syed Haider [mailto:[email protected]]
Sent: Thu 11/26/2009 8:39 AM
To: Jing, Rui
Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
Subject: Re: [mart-dev] errors when starting martview



Hi Rui,


the only critical error is :

Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf:
Invalid command 'PerlOptions', perhaps misspelled or defined by a module not
included in the server configuration


you would need to see the onscreen instrcutions when you run:

perl bin/configure.pl.....

you probably dont have mod_perl or somehting configured correctly.


Best,
Syed

Jing, Rui wrote:

Hi,

When I am starting martview, there are some error and warn, please advise

how

to

solve the problem.

[r...@]> /software/biomart-perl/apache/bin/httpd -d $PWD -f

$PWD/conf/httpd.conf

[Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in line 37 of
/common/home/hge/software/biomart-perl/conf/httpd.conf.
[Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in line 45 of
/common/home/hge/software/biomart-perl/conf/httpd.conf.
[Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in line 63 of
/common/home/hge/software/biomart-perl/conf/httpd.conf.
[Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in line 73 of
/software/biomart-perl/conf/httpd.conf.
Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf:
Invalid command 'PerlOptions', perhaps misspelled or defined by a module not
included in the server configuration


Thanks,

Ray




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