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Hello,
The error message you quoted in your message explains exactly what the
problem is:
Parent directory
(/export/system0/biomart-perl/conf/templates/default/) is not writable
The Apache process running BioMart needs to have write access to conf/,
logs/ and sessions/ folders in the biomart-perl folder and all (if any)
of their subfolders.
You need to find out what user the Apache process runs as, then use the
chmod command to grant that user write access to these folders.
cheers,
Richard
Michael Wicks wrote:
> Dear Biomart,
>
> I have successfully installed Biomart on my local machine and created
> Marts which I am very happy with. However, when I try and port my work
> to a different server, I can't get Biomart to work at all.
>
> I have copied across my registry file and ensured that my httpd.conf
> file is good after running the configure/pl script, but all I am able to
> view is the Biomart starting page. Clicking on "Start MartView Session"
> creates a 500 Internal Server error message. I include as an attachment
> the relevant error message from the apache error log. Can anybody tell
> me what I am doing wrong? (Naturally, I will supply any other resources
> to help solve this problem)
>
> Many thanks
> Mike Wicks
>
>
> ------------------------------------------------------------------------
>
>
> ERROR: caught BioMart::Exception::Template: Error in processing template
> main.tt: file error - cache failed to write main.ttc: Error in tempfile()
> using /export/system0/biomart-perl/conf/templates/default/XXXXXXXXXX: Parent
> directory (/export/system0/biomart-perl/conf/templates/default/) is not
> writable
> at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Template/Document.pm
> line 295
>
> Stacktrace:
> Exception::Class::Base::throw
> /export/system0/biomart-perl/lib/BioMart/Web.pm:257
> BioMart::Web::process_template
> /export/system0/biomart-perl/lib/BioMart/Web.pm:2302
> BioMart::Web::handle_request
> /export/system0/biomart-perl/cgi-bin/martview:73
> (eval) /export/system0/biomart-perl/cgi-bin/martview:72
>
> ModPerl::ROOT::ModPerl::Registry::export_system0_biomart_2dperl_cgi_2dbin_martview::handler
>
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:203
> (eval)
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:203
> ModPerl::RegistryCooker::run
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:169
> ModPerl::RegistryCooker::default_handler
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:30
> ModPerl::Registry::handler -e:0
> (eval) -e:0
> Use of uninitialized value in concatenation (.) or string at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Template/Provider.pm
> line 565.
> compiled template : Can't locate
> //export/system0/biomart-perl/conf/templates/default/error.ttc in @INC (@INC
> contains: /export/system0/biomart-perl/lib
> /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl . /opt/apache) at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Template/Provider.pm
> line 564.
>
> [Thu Dec 13 13:43:23 2007] [error] Error in processing template error.tt:
> file error - cache failed to write error.ttc: Error in tempfile() using
> /export/system0/biomart-perl/conf/templates/default/XXXXXXXXXX: Parent
> directory (/export/system0/biomart-perl/conf/templates/default/) is not
> writable\n at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Template/Document.pm
> line 295\n\n\nTrace begun at /export/system0/biomart-perl/lib/BioMart/Web.pm
> line 257\nBioMart::Web::process_template('BioMart::Web=HASH(0x2ddb170)',
> 'error.tt', 'HASH(0x35e9a70)') called at
> /export/system0/biomart-perl/cgi-bin/martview line
> 99\nModPerl::ROOT::ModPerl::Registry::export_system0_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x35c1410)')
> called at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm
> line 203\neval {...} at
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm
> line 203\nModPerl::RegistryC
ooker::run('ModPerl::Registry=HASH(0x35c1500)') called at
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm
line
169\nModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x35c1500)')
called at
/usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm
line 30\nModPerl::Registry::handler('ModPerl::Registry',
'Apache2::RequestRec=SCALAR(0x35c1410)') called at -e line 0\neval {...} at -e
line 0\n
- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416
http://www.biomart.org/
http://www.biojava.org/
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