On 6 Mar 2007, at 09:11, Giulia De Sario wrote:
Yes i use biomart-perl/conf/registryURLPointer
-----Messaggio originale-----
Da: Arek Kasprzyk [mailto:[EMAIL PROTECTED]
Inviato: martedì 6 marzo 2007 9.59
A: Giulia De Sario
Oggetto: Re: R: R: R: Biomart problem
On 6 Mar 2007, at 07:29, Giulia De Sario wrote:
I make a connection to your registry ...
you mean ... using 'biomart-perl/conf/registryURLPointer'?
a.
Hi Giulia,
I am moving this discussion to mart-dev so we can use more expertise
there.
Basically it appears that there must be a problem outside BioMart eg.
problems
with apache, mod_perl install or some of your CPAN modules. Could you
give
us more details on the following:
We need to know the exact Perl version, Apache version, the exact
ModPerl version,
and if they were compiled from source and what flags were used to do so
Does Apache keep running after your segfaults?
could you also try to run api_examples from the script directory and
see if this works
correctly?
ei as follows: perl apiExample.pl
please remember to set your PERL5LIB to point to
/your_path/biomart-perl/lib
a.
PS. I enclose all the info so far below:
error_log:
[Mon Mar 5 15:43:25 2007] [notice] child pid 16439 exit signal
Segmentation fault (11)
compiled in modules:
When i do "httpd -l"
The output produced is
Compiled-in modules:
http_core.c
mod_env.c
mod_log_config.c
mod_mime.c
mod_negotiation.c
mod_status.c
mod_include.c
mod_autoindex.c
mod_dir.c
mod_cgi.c
mod_asis.c
mod_imap.c
mod_actions.c
mod_userdir.c
mod_alias.c
mod_access.c
mod_auth.c
mod_setenvif.c
mod_gzip.c
mod_php4.c
mod_perl.c
suexec: disabled; invalid wrapper /var/www/bin/suexec
httpd.conf:
User biouser
Group biogroup
PidFile logs/httpd.pid
Timeout 300
KeepAlive On
MaxKeepAliveRequests 100
KeepAliveTimeout 15
MinSpareServers 2
MaxSpareServers 2
StartServers 2
MaxClients 50
MaxRequestsPerChild 0
Listen 5555
DirectoryIndex index.html
TypesConfig conf/mime.types
DefaultType text/plain
AddType image/gif .gif
AddType image/png .png
AddType image/jpeg .jpg .jpeg
AddType text/css .css
AddType text/html .html .htm
AddType text/plain .asc .txt
AddType application/pdf .pdf
AddType application/x-gzip .gz .tgz
AddType application/vnd.ms-excel .xls
ErrorLog logs/error_log
LogLevel warn
LogFormat "%h %l %u %t \"%r\" %>s %b" combined
CustomLog logs/access_log combined
<Perl>
use lib '/opt/glite/lib/perl5';
use lib '/opt/gpt/lib/perl';
use lib '/opt/glite/lib/perl5';
use lib '/opt/gpt/lib/perl';
use lib '/opt/glite/lib/perl5';
use lib '/opt/gpt/lib/perl';
use lib '/opt/glite/lib/perl5';
use lib '/opt/gpt/lib/perl';
use lib '/biotools/GD-2.32';
use lib '/biotools/Pl_Modules/';
use lib
'/biotools/Pl_Modules/i386-linux-thread-multi/';
use lib
'/biotools/analysis-interfaces/biomart-perl/lib';
require "BioMart/Configuration/Attribute.pm";
require
"BioMart/Configuration/AttributeCollection.pm";
require
"BioMart/Configuration/AttributeGroup.pm";
require
"BioMart/Configuration/AttributeList.pm";
require
"BioMart/Configuration/AttributeTree.pm";
require "BioMart/Configuration/BaseFilter.pm";
require
"BioMart/Configuration/BooleanFilter.pm";
require
"BioMart/Configuration/ConfigurationTree.pm";
require "BioMart/Configuration/DBLocation.pm";
require
"BioMart/Configuration/FilterCollection.pm";
require "BioMart/Configuration/FilterGroup.pm";
require "BioMart/Configuration/FilterList.pm";
require "BioMart/Configuration/FilterTree.pm";
require "BioMart/Configuration/Location.pm";
require
"BioMart/Configuration/MartDBLocation.pm";
require
"BioMart/Configuration/MartURLLocation.pm";
require "BioMart/Configuration/Option.pm";
require "BioMart/Configuration/PushAction.pm";
require
"BioMart/Configuration/RegistryDBPointer.pm";
require
"BioMart/Configuration/RegistryURLPointer.pm";
require "BioMart/Configuration/URLLocation.pm";
require "BioMart/Configuration/ValueFilter.pm";
require
"BioMart/Configuration/VirtualSchema.pm";
require "BioMart/AttributeTable.pm";
require "BioMart/Configurator.pm";
require "BioMart/DatasetI.pm";
require "BioMart/Exception.pm";
require "BioMart/FormatterI.pm";
require "BioMart/Initializer.pm";
require "BioMart/Links.pm";
require "BioMart/Query.pm";
require "BioMart/QueryRunner.pm";
require "BioMart/Registry.pm";
require "BioMart/ResultTable.pm";
require "BioMart/Root.pm";
require "BioMart/RootI.pm";
require "BioMart/Web.pm";
require
"BioMart/Dataset/GenomicSequence/DNAAdaptor.pm";
require "BioMart/Dataset/GenomicAlign.pm";
require "BioMart/Dataset/GenomicMAlign.pm";
require "BioMart/Dataset/GenomicSequence.pm";
require "BioMart/Dataset/GenomicSequenceMod.pm";
require "BioMart/Dataset/TableSet.pm";
require "BioMart/Formatter/AXTPLUS.pm";
require "BioMart/Formatter/ADF.pm";
require "BioMart/Formatter/AXT.pm";
require "BioMart/Formatter/FASTA.pm";
require "BioMart/Formatter/CSV.pm";
require "BioMart/Formatter/FASTAA.pm";
require "BioMart/Formatter/FASTACDNA.pm";
require "BioMart/Formatter/FASTAH.pm";
require "BioMart/Formatter/GFF.pm";
require "BioMart/Formatter/HTML.pm";
require "BioMart/Formatter/MAF.pm";
require "BioMart/Formatter/MAF_NOPREVIEW.pm";
require "BioMart/Formatter/MAF_RESTRICTED.pm";
require "BioMart/Formatter/MFA.pm";
require "BioMart/Formatter/MFASTA.pm";
require "BioMart/Formatter/TSV.pm";
require "BioMart/Formatter/TXT.pm";
require "BioMart/Formatter/XLS.pm";
require "BioMart/Web/CGIXSLT.pm";
require "BioMart/Web/PageStub.pm";
require "BioMart/Web/SiteDefs.pm";
require "BioMart/Web/TemplateBuilder.pm";
require "BioMart/Web/Zlib.pm";
#warn "MartView:: Initializing master Mart registry";
eval { my $init =
BioMart::Initializer->new(registryFile =>
'/biotools/analysis-interfaces/biomart-perl/conf/
registryURLPointer.xml');
$main::BIOMART_REGISTRY = $init->getRegistry() || die
"Can't get registry from initializer";
};
</Perl>
<IfModule mod_gzip.c>
mod_gzip_on Yes
mod_gzip_can_negotiate Yes
mod_gzip_static_suffix .gz
AddEncoding gzip .gz
mod_gzip_update_static No
mod_gzip_command_version '/mod_gzip_status'
mod_gzip_temp_dir /tmp
mod_gzip_keep_workfiles No
mod_gzip_handle_methods GET POST
mod_gzip_dechunk yes
mod_gzip_min_http 1000
mod_gzip_minimum_file_size 1000
mod_gzip_maximum_file_size 3000000
mod_gzip_maximum_inmem_size 60000
# which files are to be compressed?
#
# The order of processing during each of both
phases is not important,
# but to trigger the compression of a request's
content this request
# a) must match at least one include rule in
each of both phases and
# b) must not match an exclude rule in any of
both phases.
# These rules are not minimal, they are meant
to serve as example only.
#
# phase 1: (reqheader, uri, file, handler)
# ========================================
# (see chapter about caching for problems when
using 'reqheader' type
# filter rules.)
# NO: special broken browsers which request
for gzipped content
# but then aren't able to handle it
correctly
mod_gzip_item_exclude reqheader
"User-agent: Mozilla/4.0[678]"
#
# JA: HTML-Dokumente
mod_gzip_item_include file \.html$
mod_gzip_item_include file
\.biomart$
mod_gzip_item_include uri .
#
# NO: include files / JavaScript & CSS (due
to Netscape4 bugs)
mod_gzip_item_exclude file \.js$
mod_gzip_item_exclude file \.css$
mod_gzip_item_exclude file \.gz$
mod_gzip_item_exclude file \.xls$
#
# YES: CGI scripts
mod_gzip_item_include file \.pl$
mod_gzip_item_include handler
^cgi-script$
#
# phase 2: (mime, rspheader)
# ===========================
# YES: normal HTML files, normal text files,
Apache directory listings
#mod_gzip_item_include mime
^text/html$
#mod_gzip_item_include mime
^text/plain$
#mod_gzip_item_include mime
^httpd/unix-directory$
mod_gzip_item_include mime .
#mod_gzip_item_include mime
^application/vnd.ms-excel
#
# NO: images (GIF etc., will rarely ever save
anything)
mod_gzip_item_exclude mime ^image/
mod_gzip_send_vary Yes
</IfModule>
DocumentRoot "/biotools/analysis-interfaces/biomart-perl/htdocs"
<Location />
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Location>
ScriptAlias /biomart
"/biotools/analysis-interfaces/biomart-perl/cgi-bin"
<Location /biomart/martview>
AllowOverride None
Options None
Order allow,deny
Allow from all
SetHandler perl-script
PerlHandler Apache::Registry
Options +ExecCGI
</Location>
<Location /biomart/martservice>
AllowOverride None
Options None
Order allow,deny
Allow from all
SetHandler perl-script
PerlHandler Apache::Registry
Options +ExecCGI
</Location>
<Location /biomart/martresults>
AllowOverride None
Options None
Order allow,deny
Allow from all
SetHandler perl-script
PerlHandler Apache::Registry
Options +ExecCGI
</Location>
<Location /biomart/perl-status>
SetHandler perl-script
PerlHandler Apache::status
</Location>
The connection to my database server is the next step, if the other
things
Run right.
Thank you
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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