Hi Steffen would you like to try biomart-perl 0.6 ? or for some reason, you must stay with 0.5 ? we are happy to guide you through any of the versions, however 0.6 is much neat in terms of interface and installation.
thanks syed On Tue, 2008-02-12 at 15:30 +0100, sneumann wrote: > Hi, > > I successfully am running a biomart 0.5 on a Ubuntu Dapper, > for various reasons I am consolidating several sites > and would like to migrate martview, too. > > The target will be a Ubuntu Heron. > I tried simply copying the httpd.conf, > pointing to the NFS mounted biomart-perl. > Upon startup I get > > Syntax error on line 13 of /etc/apache2/sites-enabled/030-biomart: > Can't call method "settingsParams" on an undefined value at > /vol/methouse/biomart-perl/lib/BioMart/Initializer.pm line 639.\n > > The troubleshooting guide mentions that this might be related > to the mod_perl installation, but I followed > https://bugs.launchpad.net/ubuntu/+source/libapache2-mod-perl2/+bug/55464 > and indeed a simple test.pl can be seen in the browser. > > If I copy the <perl> ... </perl> snippet from httpd.conf > into a new file test.pl, I can run it as www-data without problems. > > If I try to re-generate the configuration, I get the error below. > One curious thing is that it won't find a dataset name > BioMart::Dataset::: Can't locate BioMart/Dataset/.pm > Indeed, the includeDatasets is empty in my registry, > but it works on the other installation ?! > > I can also see the cached configuration if I start apache > on the other host: > biomart-perl/conf/Cached/default/XML/msbi_mart_1.litlist.default > biomart-perl/conf/Cached/default/XML/msbi_mart_1.xcms.default > > My working assumption is that one of the dependencies is too new > in Heron, so I am happy to take advice which that might be, > and how to continue debugging. I also checked the postgres access, > and that _seems_ to be working. > > Yours, > Steffen > > ------------------------------------------------- > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE MartRegistry> > <MartRegistry> > > <MartDBLocation > name = "msbi_mart_1" > displayName = "MSBI Metabolites" > databaseType = "postgres" > host = "kons" > port = "5432" > database = "biomart" > schema = "public" > user = "biomart" > password = "XXX" > visible = "1" > default = "" > includeDatasets = "" > martUser = "" > /> > </MartRegistry> > > > > > ------------------------------------------------- > > perl bin/configure.pl --clean -r conf/defaultMartRegistry.xml > > Do you want to install in API only mode [y/n] [n]: > Checking prerequisites ...[Looks good] > DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n > Checking several common Apache locations...done. > Select either one of the detected httpd paths on the list, OR enter the path > you wish to use: > /usr/sbin/apache2 > [1]: > Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl > configuration > Have Apache DSO-support and ModPerl library file present, configuring ModPerl > in httpd.conf. > Enter the server host OR default [msbi]: > Enter the server port OR default [5555]: > Enter proxy OR default : > Enter the required script location OR default [biomart]: > Libdir /vol/methouse/biomart-perl/lib is not in @INC, adding to @INC > > Use of uninitialized value in sprintf at > /vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1184. > > ERROR something wrong with your registry: could not load module > BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC contains: > /vol/methouse/biomart-perl/bin/../lib /etc/perl /usr/local/lib/perl/5.8.8 > /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 > /usr/share/perl/5.8 /usr/local/lib/site_perl .) at (eval 145) line 3. > > Trace begun at /vol/methouse/biomart-perl/bin/../lib/BioMart/Root.pm line 169 > BioMart::Root::loadModule('BioMart::Initializer=HASH(0x23fac00)', > 'BioMart::Dataset::') called at > /vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1187 > BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x23fac00)') > called at /vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line > 244 > BioMart::Initializer::_init('BioMart::Initializer=HASH(0x23fac00)', > 'registryFile', '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml', > 'action', 'clean', 'mode', 'memory') called at > /vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393 > BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x23fac00)', > 'registryFile', '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml', > 'action', 'clean', 'mode', 'memory') called at > /vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 160 > BioMart::Initializer::_new('BioMart::Initializer=HASH(0x23fac00)', > 'registryFile', '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml', > 'action', 'clean', 'mode', 'memory') called at > /vol/methouse/biomart-perl/bin/../lib/BioMart/RootI.pm line 42 > BioMart::RootI::new('BioMart::Initializer', 'registryFile', > '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml', 'action', 'clean', > 'mode', 'memory') called at > /vol/methouse/biomart-perl/bin/configureBioMart.pl line 339 > eval {...} at /vol/methouse/biomart-perl/bin/configureBioMart.pl line 338 > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
