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/martDBLocation.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/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. 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