> -----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.
It looks fine when you start apache. Please try this URL instead: http://node01.com:8011/biomart/martview or just try this one http://node01.com:8011/ (there is a link on this page that takes you to martview). That should work. Cheers, Junjun > > 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 > >>> > >>> > >>> > >>> > >>> 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. > >>> > >> > > > > > > >
