On 11-08-19 11:25 AM, "Dirk Paul" <[email protected]> wrote:
>Hi Elena, > >Thanks for your email! > >I would like to use the Biomart Perl API. I followed the installation as >described here: http://www.biomart.org/user-docs.pdf. I tried to install >Apache, but I got an error message: > >wget http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz >--2011-08-19 15:52:20-- >http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz >Resolving wwwcache.sanger.ac.uk... 172.18.24.2, 172.18.24.1 Connecting >to wwwcache.sanger.ac.uk|172.18.24.2|:3128... connected. >Proxy request sent, awaiting response... 404 Not Found >2011-08-19 15:52:20 ERROR 404: Not Found. > >Maybe I don't need to install this part and ModPerl? Anyways, when I try >to install the Perl API and MartView together, I got the following error >message (see below). Please advise! > >Many thanks, Dirk. > >*** > >perl bin/configure.pl -r conf/registryURLPointer.xml > >Do you want to install in API only mode [y/n] [n]: n > >Checking prerequisites ...[Looks good] >Use of uninitialized value in string ne at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 111. >Use of uninitialized value in regexp compilation at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 113. > >rm /nfs/users/nfs_d/dp5/src/biomart-perl/conf/templates/default/*.ttcrm: >cannot remove >`/nfs/users/nfs_d/dp5/src/biomart-perl/conf/templates/default/*.ttc': No >such file or directory > >APACHE: /usr/sbin/httpd >HOST: test.biomart.org >PORT: 9002 >PROXY: >LOCATION: biomart >APXS/2: > >You can change the above configuration by editing >"biomart-perl/conf/settings.conf" > > > >No valid httpd binary specified, skipping Apache version and mod_perl >checks. No > httpd.conf will be generated. >Use of uninitialized value in string eq at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 212. >Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC Libdir >/nfs/users/nfs_d/dp5/src/biomart-perl/lib is not in @INC, adding to @INC >Use of uninitialized value in string eq at bin/ConfBuilder.pm line 89. >Use of uninitialized value in string eq at bin/ConfBuilder.pm line 133. >Use of uninitialized value in string eq at bin/ConfBuilder.pm line 225. >Use of uninitialized value in string eq at bin/ConfBuilder.pm line 225. > >Cached Registry Unavailable... > >Running Complete Clean... > > >Problems with the web server: 403 Proxy Configuration required > > > > >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 >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm >line 254 >BioMart::Initializer::_init('BioMart::Initializer=HASH(0x2551670)', >'registryFile', >'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml', >'action', 'cached', 'mode', 'memory') called at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm >line 377 >BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x2551670)', >'registryFile', >'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml', >'action', 'cached', 'mode', 'memory') called at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm >line 328 >BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x2551670)' >, 'registryFile', >'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml', >'action', 'cached', 'mode', 'memory') called at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm >line 168 >BioMart::Initializer::_new('BioMart::Initializer=HASH(0x2551670)', >'registryFile', >'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml', >'action', 'cached', 'mode', 'memory') called at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/RootI.pm line >64 BioMart::RootI::new('BioMart::Initializer', 'registryFile', >'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml', >'action', 'cached', 'mode', 'memory') called at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 332 >eval {...} at >/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 331 > > > >-----Original Message----- >From: Elena Rivkin [mailto:[email protected]] >Sent: 19 August 2011 16:19 >To: Dirk Paul >Subject: Re: [Ensembl #228924] Set up environment for Ensembl BioMart >Perl API > >Can you please post your question again? >Thank you. >Elena Rivkin, PhD >Outreach and Training Coordinator, Informatics and Bio-computing > >Ontario Institute for Cancer Research >MaRS Centre, South Tower >101 College Street, Suite 800 >Toronto, Ontario, Canada M5G 0A3 > >Tel: 647-258-4316 >Toll-free: 1-866-678-6427 >www.oicr.on.ca > >This message and any attachments may contain confidential and/or >privileged information for the sole use of the intended recipient. Any >review or distribution by anyone other than the person for whom it was >originally intended is strictly prohibited. If you have received this >message in error, please contact the sender and delete all copies. >Opinions, conclusions or other information contained in this message may >not be that of the organization. > > > > > > >On 11-08-19 11:05 AM, "Bert Overduin via RT" <[email protected]> >wrote: > >>Hello Dirk Paul, >> >>I am forwarding your question to the BioMart group at OICR, as we are >not >>the right people to ask these technical questions, I am afraid. >> >>-- >>With kind regards, >>Bert Overduin, Ph.D. >>(Ensembl Helpdesk) >> >>Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html >>Blog: http://www.ensembl.info >>YouTube: http://www.youtube.com/user/EnsemblHelpdesk >>Facebook: http://www.facebook.com/Ensembl.org >>Twitter: http://twitter.com/Ensembl >> >> >> >>-- >> The Wellcome Trust Sanger Institute is operated by Genome Research >> Limited, a charity registered in England with number 1021457 and a >> company registered in England with number 2742969, whose registered >> office is 215 Euston Road, London, NW1 2BE. > > > >-- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
