[ensembl-dev] a caching question?

Jay Humphrey jhumphre at ebi.ac.uk
Thu Apr 26 09:17:20 BST 2012


Yes, there is caching of the source code.  You woul have to restart the 
server every time you make a change, or add Apache2::Reload to the 
apache/mod_perl configuration.
In conf/httpd.conf, just before the <Perl> section, add:

PerlModule Apache2::Reload
PerlInitHandler Apache2::Reload
PerlSetEnv PERL5LIB [insert your entire PERL5LIB here including all of 
the Ensembl modules directories]
#for example:
#PerlSetEnv PERL5LIB PerlSetEnv PERL5LIB 
/path/to/ensembl/eg-plugins/fungi/modules:/path/to/ensembl/eg-plugins/blast/modules:/path/to/ensembl/eg-plugins/common/modules:/path/to/ensembl/plubic-plugins/orm/modules:/path/to/ensembl/ebi-plugins/admin/modules:/path/to/ensembl/public-plugins/admin/modules:/path/to/ensembl/public-plugins/ensembl/modules:/path/to/perl/bioperl-extra:/path/to/perl/msatools:/path/to/perl/perllib2:/path/to/perl/bioperl-1.2.3:/path/to/perl/vcftools/lib:/path/to/perl/perllib2/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi:/path/to/perl/perllib2/x86_64-linux-thread-multi:/path/to/perl/perllib2/lib/perl5/site_perl/5.8.8:/path/to/ensembl/apache2lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/:/path/to/ensembl/ensembl/modules:/path/to/ensembl/ensembl-compara/modules:/path/to/ensembl/ensembl-draw/modules:/path/to/ensembl/ensembl-variation/modules:/path/to/ensembl/ensembl-functgenomics/modules:/path/to/ensembl/ensembl-external/modules:/path/to/ensembl/biomart-perl/lib:/path/to/ensembl/bioperl-live:/path/to/ensembl/mini-bioperl-161:/path/to/ensembl/modules:/path/to/ensembl/utils/../:/path/to/ensembl/utils/../conf:/usr/lib64/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/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/vendor_perl/5.8.8:/usr/lib/perl5/vendor_perl:/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi:/usr/lib/perl5/5.8.8:.

On 26/04/2012 00:01, Thomason, James wrote:
> Gang,
>
> I'm working on another exporting gimmick and am having trouble. I've mostly tracked it down, but am trying to isolate what looks like a bug to me. My issue is that no matter where I seem to add in debugging code to ensembl to trace it back, it's never getting executed. I'm trying to add some debugging lines to EnsEMBL::Web::Component, but nothing's showing up.
>
> So my questions -
> 1) Is there some cache that's butting in here? And, can I clear it out easily enough?
> or
> 2) Is there some other file I should be editing instead? A plugin or something?
>
> Many thanks, as always.
>
> --
> -Jim Thomason...
>
> Scientific Informatics Developer @ The Ware Lab,
> a USDA-ARS Laboratory at Cold Spring Harbor Laboratory
> http://www.warelab.org/
> http://www.cshl.edu/
>
>
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-- 
Jay Humphrey                   Ensembl Genomes Web Developer
EMBL-EBI                       Tel: +44-(0)1223-492682
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






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