-----Original Message-----
From: Jing, Rui [mailto:[email protected]]
Sent: Thursday, December 03, 2009 12:13 AM
To: Syed Haider
Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
Subject: RE: [mart-dev] errors when starting martview
Hi Syed,
when I ran, it gave the following info.
/common/home/software/biomart-perl/apache/bin/httpd -d $PWD -f
$PWD/conf/httpd.conf
Processing Cached Registry:
/common/home/software/biomart-perl/conf/cachedRegistries/martD
BLocation.xml.cach
ed
then I try to visit biomart
http://node01.com:8011/biomart-perl/martview
it does not work.
Could you please let me know what the problem is?
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/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/martD
BLocation.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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