Hi Junjun, It works when I ran the command. what is the problem with martDBLocation.xml running? I want to have local biomart server. Could you please let me know if my settings.conf and registryURLPointer.xml is correct. what is the reason with the errors? Thank you so much, Ray [r...@promoter biomart-perl]# mysql -hmartdb.ebi.ac.uk -uanonymous -P3306 msd_mart_4 Reading table information for completion of table and column names You can turn off this feature to get a quicker startup with -A Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 167098 to server version: 5.0.41-log Type 'help;' or '\h' for help. Type '\c' to clear the buffer. mysql>
________________________________ From: Junjun Zhang [mailto:[email protected]] Sent: Thu 10/29/2009 1:36 PM To: Jing, Rui; [email protected] Subject: RE: [mart-dev] The problem with Biomart installation - need your help Hi Ray, Now the error is slightly different, it shows that you can not connect to the database specified in martDBLocation.xml: > COULD NOT CONNECT TO DATABASE msd_mart_4.CHECK YOUR SETTINGS Please, in the command line try the following: mysql -hmartdb.ebi.ac.uk -uanonymous -P3306 msd_mart_4 If it fails, it may be that the port (3306) is blocked (and if that's the case please contact your network admin). Let me know how it goes. Cheers, Junjun > -----Original Message----- > From: Jing, Rui [mailto:[email protected]] > Sent: Thursday, October 29, 2009 11:40 AM > To: Junjun Zhang; Jianxin Wang; [email protected] > Subject: RE: [mart-dev] The problem with Biomart installation > - need your help > > Hi Junjun, > > The same problem when I ran: perl bin/configure.pl -r > conf/martDBLocation.xml. > Please let me know what the problem is. do I need to change > martDBLocation.xml? > Thanks, > > the content of my conf files: > 1. martDBLocation.xml > <MartRegistry> > <MartDBLocation > name = "msd_mart_4" > displayName = "My BioMart Database" > databaseType = "mysql" > host = "martdb.ebi.ac.uk" > port = "3306" > database = "msd_mart_4" > schema = "msd_mart_4" > user = "anonymous" > password = "" > visible = "1" > default = "" > includeDatasets = "" > martUser = "" > /> > </MartRegistry> > > 2. settings.conf > [httpdSettings] > apacheBinary=/usr/local/apache/bin/httpd > serverHost=promoter.dfci.harvard.edu > port=80 > # to use proxying set the proxy port below (even if its 80) > and set serverHost as your proxy host proxy= # if apxs or > apxs2 is not in default directory where httpd lives, you may > set this param to point to apxs/2 apxs= location=biomart-perl > > > [r...@promoter biomart-perl]# perl bin/configure.pl -r > conf/martDBLocation.xml Do you want to install in API only > mode [y/n] [n]: > Checking prerequisites ...[Looks good] > Use of uninitialized value in string ne at > /home/software/biomart-perl/bin/configureBioMart.pl line 110. > Use of uninitialized value in regexp compilation at > /home/software/biomart-perl/bin/configureBioMart.pl line 112. > rm > /home/software/biomart-perl/conf/templates/default/*.ttcrm: > cannot remove > `/home/software/biomart-perl/conf/templates/default/*.ttc': > No such file or directory > APACHE: /usr/local/apache/bin/httpd > HOST: promoter.dfci.harvard.edu > PORT: 80 > PROXY: > LOCATION: biomart-perl > APXS/2: > You can change the above configuration by editing > "biomart-perl/conf/settings.conf" > > Got usable Apache in /usr/local/apache/bin/httpd, probing for > version & ModPerl configuration Libdir > /home/software/biomart-perl/lib is not in @INC, adding to > @INC Cached Registry Unavailable... > Running Complete Clean... > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!!!! > > COULD NOT CONNECT TO DATABASE msd_mart_4.CHECK YOUR SETTINGS > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!!!!! > > > ERROR something wrong with your registry: Problems with the > retrieval of dataset configuration > Please check: > that your mart Registry files contains correct > connection params, > > that you are using the correct version on XML::Simple, > that BioMart databases contain a populated > meta_conf tables and > that you have set martUser correctly if you > are running in restricted data > access mode (populated meta_conf__user__dm) > > Trace begun at > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > line 254 > BioMart::Initializer::_init('BioMart::Initializer=HASH(0x15eb8150)', > 'registryFile', > '/home/software/biomart-perl/conf/martDBLocation.xml', > 'action', 'cached', 'mode', 'memory') called at > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > line 377 > BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x > 15eb8150)', > 'registryFile', > '/home/software/biomart-perl/conf/martDBLocation.xml', > 'action', 'cached', 'mode', 'memory') called at > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > line 328 > BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0 > x15eb8150)', > 'registryFile', > '/home/software/biomart-perl/conf/martDBLocation.xml', > 'action', 'cached', 'mode', 'memory') called at > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > line 168 > BioMart::Initializer::_new('BioMart::Initializer=HASH(0x15eb8150)', > 'registryFile', > '/home/software/biomart-perl/conf/martDBLocation.xml', > 'action', 'cached', 'mode', 'memory') called at > /home/software/biomart-perl/bin/../lib/BioMart/RootI.pm line > 64 BioMart::RootI::new('BioMart::Initializer', > 'registryFile', > '/home/software/biomart-perl/conf/martDBLocation.xml', > 'action', 'cached', 'mode', 'memory') called at > /home/software/biomart-perl/bin/configureBioMart.pl > line 331 > eval {...} at > /home/software/biomart-perl/bin/configureBioMart.pl line 330 > > Thanks, > > Ray > > ________________________________ > > From: Junjun Zhang [mailto:[email protected]] > Sent: Thu 10/29/2009 10:47 AM > To: Jing, Rui; Jianxin Wang; [email protected] > Subject: RE: [mart-dev] The problem with Biomart installation > - need your help > > > > Hi Ray, > > Thanks for sending us the registry. > > Since you are first time biomart user, I do not encourage you > use 'RegistryURLPointer' in your registry file. Rather, > please use one of the registry examples under 'conf' > directory, for example, martDBLocation.xml. After you run > bin/configure.pl with this registry file successfully, then > you know the installation is OK. > > Let us know how it goes. > > Kind regards, > Junjun > > > > > > > -----Original Message----- > > From: [email protected] > > [mailto:[email protected]] On Behalf Of Jing, Rui > > Sent: Thursday, October 29, 2009 9:46 AM > > To: Jianxin Wang; [email protected] > > Subject: RE: [mart-dev] The problem with Biomart installation > > - need your help > > > > Hi Jason, > > > > Here is my registryuRLPointer.xml > > > > <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE MartRegistry> > > <MartRegistry> <RegistryURLPointer > > name = "central_server" > > host = "promoter.dfci.harvard.edu" > > port = "80" > > path = "" > > includeMarts = "msd,uniprot" > > /> > > </MartRegistry> > > > > Thanks, > > > > Rui > > > > ________________________________ > > > > From: Jianxin Wang [mailto:[email protected]] > > Sent: Wed 10/28/2009 6:40 PM > > To: Jing, Rui; [email protected] > > Subject: RE: [mart-dev] The problem with Biomart installation > > - need your help > > > > > > > > Hi Jing, > > > > Could you send us your registry.xml file? In your case the > > "registryuRLPointer.xml"? > > > > Jason > > ________________________________________ > > From: [email protected] [[email protected]] > On Behalf Of > > Jing, Rui [[email protected]] > > Sent: Wednesday, October 28, 2009 4:02 PM > > To: [email protected] > > Subject: RE: [mart-dev] The problem with Biomart installation > > - need your help > > > > Hi, > > > > I am trying to install Biomart. When running perl > bin/configure.pl -r > > conf/registryURLPointer.xml I get the following error message: > > > > Checking prerequisites ...[Looks good] Use of uninitialized > value in > > string ne at > /home/software/biomart-perl/bin/configureBioMart.pl line > > 110. > > Use of uninitialized value in regexp compilation at > > /home/software/biomart-perl/bin/configureBioMart.pl line 112. > > rm > > /home/software/biomart-perl/conf/templates/default/*.ttcrm: > > cannot remove > > `/home/software/biomart-perl/conf/templates/default/*.ttc': > > No such file or directory > > APACHE: /usr/local/apache/bin/httpd > > HOST: promoter > > PORT: 80 > > PROXY: > > LOCATION: biomart-perl > > APXS/2: > > You can change the above configuration by editing > > "biomart-perl/conf/settings.conf" > > > > Got usable Apache in /usr/local/apache/bin/httpd, probing > for version > > & ModPerl configuration Libdir > /home/software/biomart-perl/lib is not > > in @INC, adding to @INC Cached Registry Unavailable... > > Running Complete Clean... > > > > Problems with the web server: 404 Not Found > > > > > > ERROR something wrong with your registry: Problems with > the retrieval > > of dataset configuration > > Please check: > > that your mart Registry files contains correct > > connection params, > > > > that you are using the correct version on > XML::Simple, > > that BioMart databases contain a populated > meta_conf > > tables and > > that you have set martUser correctly if you > are running > > in restricted data > > access mode (populated meta_conf__user__dm) > > > > Trace begun at > > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > > line 254 > > BioMart::Initializer::_init('BioMart::Initializer=HASH(0xcf381e0)', > > 'registryFile', > > '/home/software/biomart-perl/conf/registryURLPointer.xml', > > 'action', 'cached', 'mode', 'memory') called at > > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > > line 377 > > BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x > > cf381e0)', > > 'registryFile', > > '/home/software/biomart-perl/conf/registryURLPointer.xml', > > 'action', 'cached', 'mode', 'memory') called at > > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > > line 328 > > BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0 > > xcf381e0)', > > 'registryFile', > > '/home/software/biomart-perl/conf/registryURLPointer.xml', > > 'action', 'cached', 'mode', 'memory') called at > > /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm > > line 168 > > BioMart::Initializer::_new('BioMart::Initializer=HASH(0xcf381e0)', > > 'registryFile', > > '/home/software/biomart-perl/conf/registryURLPointer.xml', > > 'action', 'cached', 'mode', 'memory') called at > > /home/software/biomart-perl/bin/../lib/BioMart/RootI.pm line > > 64 BioMart::RootI::new('BioMart::Initializer', > > 'registryFile', > > '/home/software/biomart-perl/conf/registryURLPointer.xml', > > 'action', 'cached', 'mode', 'memory') called at > > /home/software/biomart-perl/bin/configureBioMart.pl > > line 331 > > eval {...} at > > /home/software/biomart-perl/bin/configureBioMart.pl line 330 > > > > thanks, > > > > Ray > > > > ________________________________ > > > > From: [email protected] on behalf of Jing, Rui > > Sent: Wed 10/28/2009 2:10 PM > > To: [email protected] > > Subject: [mart-dev] The problem with Biomart installation - > need your > > help > > > > > > > > Hi > > > > I am trying to install Biomart. When running perl > bin/configure.pl -r > > conf/registryURLPointer.xml I get the following error message: > > > > Checking prerequisites ...[Looks good] Can't locate > XML/Simple.pm in > > @INC (@INC contains: > > /home/software/biomart-perl/bin/../lib > > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > > /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi > > /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi > > /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 > > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 > > /usr/lib/perl5/site_perl > > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi > > /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi > > /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi > > /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 > > /usr/lib/perl5/vendor_perl/5.8.6 > > /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl > > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi > > /usr/lib/perl5/5.8.8 .) at > > /home/software/biomart-perl/bin/../lib/BioMart/Web.pm > > line 48. > > BEGIN failed--compilation aborted at > > /home/software/biomart-perl/bin/../lib/BioMart/Web.pm line 48. > > Compilation failed in require at (eval 15) line 3. > > ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85. > > BEGIN failed--compilation aborted at > > /home/software/biomart-perl/bin/../lib/BioMart/Web/TemplateBui > > lder.pm line 53. > > Compilation failed in require at > > /home/software/biomart-perl/bin/configureBioMart.pl line 39. > > BEGIN failed--compilation aborted at > > /home/software/biomart-perl/bin/configureBioMart.pl line 39. > > > > Please would you be able to tell me how to fix this? > > > > 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. > > > > > > > > > > > > > >
