Hi Ray: Could you please provide us with more info? Were you able to connect to msd_mart_4 from a command line (as Junjun suggested)?
Regards, Christina > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Jing, Rui > Sent: Friday, October 30, 2009 3:54 PM > To: [email protected] > Subject: RE: [mart-dev] The problem with Biomart installation > - need your help > > Hi > > who can help me to solve the problem. Thanks, > > Ray > > ________________________________ > > 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. > > > > > > > > > > > > > > > > > > > > > > > >
