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 ?
[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 >> >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine > at >> http://www.partners.org/complianceline . If the e-mail was sent to you in > error >> but does not contain patient information, please contact the sender and > properly >> dispose of the e-mail. >> > >
