Thanks and Best Regards,
Felix Natter
_________________________________________
Bayer HealthCare AG
BHC-PK
Elberfeld, 0500
Phone:
Fax:
E-mail: [EMAIL PROTECTED]
Web: http://www.bayerhealthcare.com
Vorstand: Arthur Higgins, Vorsitzender | Werner Baumann, Hartmut
Klusik, Lykele van der Broek, Gunnar Riemann
Vorsitzender des Aufsichtsrats: Richard Pott
Sitz der Gesellschaft: Leverkusen | Eintragung: Amtsgericht Köln,
HRB 49894
================================
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Syed Haider <[EMAIL PROTECTED]>
06.08.2007 19:20
An
[EMAIL PROTECTED]
Kopie
[email protected], [EMAIL PROTECTED], Arek Kasprzyk
<[EMAIL PROTECTED]>
Thema
Re: Antwort: Re:
[mart-dev]
Problems with
biomart 0.6 as
part
ofensembl
Hi Felix
nice to know that your biomart independent installation works fine.
What
From your installation process what I can remotely guess is some
paths
not being correctly mapped to the directory containing templates of
your
datasets.
please check whats in the following directory:
ls -lh biomart-perl/conf/templates/cached/
and see if all your directories have permissions assigned to apache.
In addition, the problem seems to be an ENSEMBL integration problem
and
you need to contact 'ensembl help desk' to get the best help on the
matter.
Kind Regards
Syed
On Mon, 2007-08-06 at 18:43 +0200, [EMAIL PROTECTED]
wrote:
hello Syed,
I just installed biomart 0.6 standalone and it is working. But
unfortunately I still get "ERROR: requested template missing" when
running biomart in ensembl.
here is the output of configure.pl:
[EMAIL PROTECTED]:/u1/ET/ensembl/ensembl/biomart-perl> perl
bin/configure.pl -r
conf/registryURLPointer.xml --clean
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
APACHE: /u1/ET/ensembl/ensembl/apache2/bin/httpd
HOST: localhost
PORT: 9002
Use of uninitialized value in print at
/u1/ET/ensembl/branch-ensembl-45/biomart-perl/bin/configureBioMart.pl
line 116.
PROXY:
LOCATION: biomart
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /u1/ET/ensembl/ensembl/apache2/bin/httpd,
probing
for version &
ModPerl configuration
Have Apache DSO-support and ModPerl library file present,
configuring
ModPerl in
httpd.conf.
Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
Libdir /u1/ET/ensembl/branch-ensembl-45/biomart-perl/lib is not in
@INC, adding to
@INC
Connection parameters of [UNIPROT PROTOTYPE (EBI)] [ OK ]
Connection parameters of [MSD PROTOTYPE (EBI)] [ OK ]
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... UNIPROT PROTOTYPE (EBI) .. 001/006 ... uniprot_location
.......................... (WEB) www.biomart.org:80 ............ ->
upgrading to
0.6 ... OK
default ... UNIPROT PROTOTYPE (EBI) .. 002/006 ... uniprot_sequence
.......................... (WEB) www.biomart.org:80 ............ ->
upgrading to
0.6 ... OK
default ... UNIPROT PROTOTYPE (EBI) .. 003/006 ...
uniprot_cell_component
.................... (WEB) www.biomart.org:80 ............ ->
upgrading to 0.6 ...
OK
default ... UNIPROT PROTOTYPE (EBI) .. 004/006 ...
uniprot_biol_process
...................... (WEB) www.biomart.org:80 ............ ->
upgrading to 0.6
... OK
default ... UNIPROT PROTOTYPE (EBI) .. 005/006 ... uniprot
................................... (WEB)
www.biomart.org:80 ............ ->
upgrading to 0.6 ... OK
default ... UNIPROT PROTOTYPE (EBI) .. 006/006 ...
uniprot_mol_function
...................... (WEB) www.biomart.org:80 ............ ->
upgrading to 0.6
... OK
default ... MSD PROTOTYPE (EBI) ...... 001/001 ... msd
....................................... (WEB)
www.biomart.org:80 ............ ->
upgrading to 0.6 ... OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 7/7
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/2] Attribute Panel of Dataset.. :uniprot
[1/2] Filter Panel of Dataset..... :uniprot
[2/2] Attribute Panel of Dataset.. :msd
[2/2] Filter Panel of Dataset..... :msd
========================================
this is the content of conf/settings.conf:
#########################################################
################ httpd.conf settings ####################
[httpdSettings]
#apacheBinary=/usr/sbin/httpd
apacheBinary=/u1/ET/ensembl/ensembl/apache2/bin/httpd
#serverHost=test.biomart.org
serverHost=localhost
port=9002
#port=3128
# to use proxying set the proxy port below (even if its 80) and set
serverHost as
your proxy host
#proxy=3128
location=biomart
# Colours settings for MARTVIEW
# A good online tool help with picking a palette is;
# http://slayeroffice.com/tools/color_palette/
[cssSettings]
# The default theme, based on a 6-level grey scale from black to
white.
colour_saturation0=black
colour_saturation20=black
colour_saturation40=#666666
colour_saturation60=#CCCCCC
colour_saturation80=#E5E5E5
colour_saturation100=white
# The blue theme used for WormMart
#colour_saturation0=black
#colour_saturation20=#5870A3
#colour_saturation40=#8294BA
#colour_saturation60=#D5DBE8
#colour_saturation80=#EFF1F6
#colour_saturation100=white
font_colour_top_bottom_menubar = #000
font_colour_rest = #000
summary_panel_bgcolour = #ffffdd
main_panel_bgcolour = #fff
top_bottom_menubar_bgcolour = #efefef
blocks_outline_colour = #efefef
summary_panel_highlight_border_colour = #ffd9af
summary_panel_highlight_bgcolour = #ffd9af
# These settings relate to the text displayed in the interface drop
downs
[aliases]
Schema=- CHOOSE SCHEMA -
Database=- CHOOSE DATABASE -
Dataset=- CHOOSE DATASET -
# If an attribute URL is specified relatively such as '/geneview/?=%
s'
# then by default this will be used relative to the current host
# However if you set exturl below then this will be prefixed
# to these URLs
[urlPrefixes]
exturl=http://byzvse:1235
# These settings are used to control how the background
# results jobs are managed.
#
# Set resultsDirCount to the number of results directories
# you want to use. Then, use resultsDir1, resultsDir2 etc.
# to assign names for these directories, up to resultsDirN
# where N is the value of resultsDirCount. Background jobs
# will be assigned to each of these resultsDir locations
# by a hash function which is intended to distribute them
# evenly.
#
# Use resultsDir to specify where
# files containing results from background jobs are stored.
# This folder must (a) exist and (b) be writable by the
# owner of the web server process.
#
# The enable setting should have a value of 'yes'
# if you want background jobs to be available to the user.
# Any other value, including non-lowercase versions of 'yes'
# will turn background jobs off.
[background]
resultsDirCount=1
#resultsDir1=/ebi/www/biomart/test/files
resultsDir1=/u1/ET/ensembl/ensembl/biomart-results
enable=yes
# Mail settings are used for informing users when their
# background tasks are finished. The mailerType defines
# the way in which mail is sent, as understood by
# Mail::Mailer. For details of how to control this, see:
#
# http://search.cpan.org/dist/MailTools/Mail/Mailer.pm
#
# The from address is the address that messages will
# appear to be from.
[mailSettings]
mailerType=sendmail
subject=Your BioMart results are ready
[EMAIL PROTECTED]
# These settings relate to sessions.
#
# The expire setting relates to how long sessions will live
# on disk for. If not accessed for a period of time longer than
# this, then the session will be dropped. Aliases are:
#
# +-----------+---------------+
# | alias | meaning |
# +-----------+---------------+
# | s | Second |
# | m | Minute |
# | h | Hour |
# | d | Day |
# | w | Week |
# | M | Month |
# | y | Year |
# +-----------+---------------+
#
# Driver could have values based on where you want the session to
be
# stored. default or no value assigned is set to Berkeley DB
implementation.
# All possible values could be:
# driver=
# driver=default
# driver=files
# driver=mysql
# driver=oracle
# a database table must already exist with any name but with strict
columnName/Types
# EXAMPLES
# ========== MySQL ============
# first create the table as
# CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session
LONGTEXT NOT NULL )
;
# then the following settings should follow under [sessions]
# driver=mysql
# dsn=DBI:mysql:database=YOU_DATABASE_NAME;host=127.0.0.1;port=3306
# user=root
# pass=
# ========== ORACLE ============
# first create the table as
# CREATE TABLE sessions ( id CHAR(32) NOT NULL UNIQUE, a_session
CLOB
NOT NULL ) ;
# then the following settings should follow under [sessions]
# driver=oracle
# dsn=dbi:Oracle:host=172.22.70.89;sid=XE;port=1521
# user=root
# pass=
[sessions]
expire=12h
driver=default
# Web Service Logging options
[webserviceLogging]
mode=ON
log_query=ON
log_IP=ON
=====================================================
biomart-perl/conf/error_log does not exist as I am using the ensembl
web server.
Here is the relevant part of the ensembl apache2 error log:
[Mon Aug 06 18:31:52 2007] [notice] Apache/2.2.4 (Unix)
mod_perl/2.0.3
Perl/v5.8.5 configured -- resuming normal operations
INIT WEB MODULE...
at
/u1/ET/ensembl/ensembl/public-plugins/mart/modules/BioMart/Web/
PageStub.pm line 27.
Use of uninitialized value in concatenation (.) or string
at /u1/ET/ensembl/ensembl/biomart-perl/lib/BioMart/Web.pm line 1784
\
.
INIT WEB MODULE...
at
/u1/ET/ensembl/ensembl/public-plugins/mart/modules/BioMart/Web/
PageStub.pm line 27.
These are the relevant lines in Web.pm:
my $allAttributeTrees =
$registry->getConfigTreeForDataset($dataset_name, $schema_nam\
e, 'default')->getAllAttributeTrees();
my $atttree =
$allAttributeTrees->[0]; # first one is supposed to be the default
one
$logger->debug("Got
outputformats ".$atttree." for attpage $attributepage, in dataset\
$dataset_name");
Thanks for your help and Best Regards,
Felix Natter
_________________________________________
Bayer HealthCare AG
BHC-PK
Elberfeld, 0500
Phone:
Fax:
E-mail: [EMAIL PROTECTED]
Web: http://www.bayerhealthcare.com
Vorstand: Arthur Higgins, Vorsitzender | Werner Baumann, Hartmut
Klusik, Lykele van der Broek, Gunnar Riemann
Vorsitzender des Aufsichtsrats: Richard Pott
Sitz der Gesellschaft: Leverkusen | Eintragung: Amtsgericht
Köln,
HRB 49894
================================
Die vorangehende e-mail inkl. jeglicher Anhänge beinhaltet
Informationen, die vertraulich oder nicht für die Öffentlichkeit
bestimmt sein könnten. Sie ist nur für den/die designierten
Empfänger
bestimmt. Sollten Sie nicht der designierte Empfänger sein,
informieren Sie bitte den Absender und löschen Sie die Nachricht aus
Ihrem System. Gebrauch, Verbreitung, Verteilung oder Reproduktion
dieser Nachricht sind untersagt und können rechtswidrig sein.
================================
The preceding e-mail message (including any attachments) contains
information that may be confidential, or constitute non-public
information. It is intended to be conveyed only to the designated
recipient(s). If you are not an intended recipient of this message,
please notify the sender by replying to this message and then delete
it from your system. Use, dissemination, distribution, or
reproduction of this message by unintended recipients is not
authorized and may be unlawful.
Syed Haider <[EMAIL PROTECTED]>
Gesendet von:
[EMAIL PROTECTED]
03.08.2007 12:00
An
[EMAIL PROTECTED]
Kopie
[email protected]
Thema
Re: [mart-dev]
Problems with
biomart 0.6 as
part ofensembl
Hi Felix
could you please forward me
- the onscreen response once you execute
perl bin/configure.pl -r conf/registryURLPointer.xml --clean
- your biomart-perl/conf/settings.conf
- conf/error_log
and most important of all, have you tried installing biomart
independently first and see if it works for you, then we can take a
step
forward to get this to work with Ensembl.
for instructions about how to install biomart independently, follow
DOCS
tab on www.biomart.org
for any further help, free to write back.
kind regards
syed
On Fri, 2007-08-03 at 11:51 +0200, [EMAIL PROTECTED]
wrote:
perl bin/configure.pl -r conf/registryURLPointer.xml
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
