Many thanks - once you've been bashing your head against the wall you
often can't see the wood for the trees!
I changed file permissions now and it seems to work
Many thanks
Mike W
Richard Holland wrote:
> 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::Registry
C
> 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
>
