Hi Syed,
Thanks for your speedy reply. I have included "User" and "Group"
directives to "aaron" and "aaron" respectively, that is the same owner
that owns all the contents of my (Vanilla) biomart-perl directory (I
have not yet changeed mode of any of the files).
And I did disable SELinux just reduce the variables (probable sources of
the errors) using "#/setenforce 0"/ .
Allan.
Syed Haider wrote:
Hi Allan
Please send me the on screen response when you do the following:
- perl bin/configure.pl -r con/your_registry_File.xml --clean
Mon Oct 22 13:41:36 SAST 2007
[EMAIL PROTECTED] biomart-perl]$ perl bin/configure.pl -r
conf/biomart3___postgresql.xml --clean;date;
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
Use of uninitialized value in string ne at
/var/biomart/biomart-0.6/biomart-perl/bin/configureBioMart.pl line 84.
Use of uninitialized value in regexp compilation at
/var/biomart/biomart-0.6/biomart-perl/bin/configureBioMart.pl line 86.
rm /var/biomart/biomart-0.6/biomart-perl/conf/templates/default/*.ttc
APACHE: /var/httpd/httpd-2.2.4/bin/httpd
HOST: localhost
PORT: 9002
PROXY:
LOCATION: biomart
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /var/httpd/httpd-2.2.4/bin/httpd, probing for
version & ModPerl configuration
Libdir /var/biomart/biomart-0.6/biomart-perl/lib is not in @INC, adding
to @INC
Connection parameters of [MID Biomart] [ OK ]
Connection parameters of [MID Assay Summary] [ OK ]
Connection parameters of [MID Participant Summary] [ OK ]
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... MID Biomart .............. 001/001 ... mid
....................................... (RDBMS) localhost:5432 ....... OK
default ... MID Assay Summary ........ 001/001 ... midsummary_level1
......................... (RDBMS) localhost:5432 ....... OK
default ... MID Participant Summary .. 001/001 ... midsummary
................................ (RDBMS) localhost:5432 ....... OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 3/3 - 0 remain
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/3] Attribute Panel of Dataset.. :mid
[1/3] Filter Panel of Dataset..... :mid
[2/3] Attribute Panel of Dataset.. :midsummary_level1
[2/3] Filter Panel of Dataset..... :midsummary_level1
[3/3] Attribute Panel of Dataset.. :midsummary
[3/3] Filter Panel of Dataset..... :midsummary
Mon Oct 22 13:42:49 SAST 2007
[EMAIL PROTECTED] biomart-perl]$
In addition the contents of,
- biomart-perl/conf/settings.conf
- biomart-perl/conf/httpd.conf
- restart the server
- navigate to http://your_server:9002/biomart/martview, and what appears
in logs/error_log
and please check if your apache has 'exec' rights on biomart directory.
may be you need to add apache user directive in httpd.conf manually, and
then restart the server.
cheers
syed
On Mon, 2007-10-22 at 12:46 +0200, allank wrote:
Hi all,
I am experiencing difficulties starting and running a Biomart session on
any of two servers one having fc-7 (with SELinux) and the other CentOS
(with SELinux).
I am getting the error below.
[Mon Oct 22 12:36:33 2007] [error] [client 127.0.0.1] (2)No such file or
directory: exec of
'/var/biomart/biomart-0.6/biomart-perl/cgi-bin/martview' failed,
referer: http://localhost:9002/
[Mon Oct 22 12:36:33 2007] [error] [client 127.0.0.1] Premature end of
script headers: martview, referer: http://localhost:9002/
Kindly advise,
Allan.
plain text document attachment (settings.conf)
#########################################################
################ httpd.conf settings ####################
[httpdSettings]
apacheBinary=/var/httpd/httpd-2.2.4/bin/httpd
serverHost=localhost
port=9002
# to use proxying set the proxy port below (even if its 80) and set serverHost
as your proxy host
proxy=
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
# 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://www.ensembl.org
# 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=/var/biomart/biomart-0.6/biomart-perl__MID__5558.data
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=1d
driver=default
# Web Service Logging options
[webserviceLogging]
mode=OFF
log_query=OFF
log_IP=ON
plain text document attachment (httpd.conf)
PidFile logs/httpd.pid
Timeout 300
KeepAlive On
MaxKeepAliveRequests 100
KeepAliveTimeout 15
MinSpareServers 2
MaxSpareServers 2
StartServers 2
MaxClients 50
MaxRequestsPerChild 0
Listen 9002
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/xml .xml
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
DocumentRoot "/var/biomart/biomart-0.6/biomart-perl/htdocs"
<Location />
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Location>
ScriptAlias /biomart/martview
"/var/biomart/biomart-0.6/biomart-perl/cgi-bin/martview"
<Location /biomart/martview>
AllowOverride None
Options None
Order allow,deny
Allow from all
<IfModule mod_deflate.c>
## zip both input and output
SetOutputFilter DEFLATE
SetInputFilter DEFLATE
## donot zip already zipped files
SetEnvIfNoCase Request_URI \.(?:exe|t?gz|zip|bz2|sit|rar)$ no-gzip dont-vary
</IfModule>
Options +ExecCGI
</Location>
ScriptAlias /biomart/martservice
"/var/biomart/biomart-0.6/biomart-perl/cgi-bin/martservice"
<Location /biomart/martservice>
AllowOverride None
Options None
Order allow,deny
Allow from all
Options +ExecCGI
</Location>
ScriptAlias /biomart/martresults
"/var/biomart/biomart-0.6/biomart-perl/cgi-bin/martresults"
<Location /biomart/martresults>
AllowOverride None
Options None
Order allow,deny
Allow from all
Options +ExecCGI
</Location>
ScriptAlias /biomart/das/dsn
"/var/biomart/biomart-0.6/biomart-perl/cgi-bin/dsn"
<Location /biomart/das/dsn>
AllowOverride None
Options None
Order allow,deny
Allow from all
Options +ExecCGI
</Location>
plain text document attachment (error_log)
[Mon Oct 22 12:35:40 2007] [notice] Apache/2.2.4 (Unix) configured -- resuming
normal operations [Mon Oct 22 12:36:09 2007] [error] [client 127.0.0.1] File
does not exist: /var/biomart/biomart-0.6/biomart-perl/htdocs/favicon.ico [Mon
Oct 22 12:36:16 2007] [error] [client 127.0.0.1] (2)No such file or directory:
exec of '/var/biomart/biomart-0.6/biomart-perl/cgi-bin/martview' failed,
referer: http://localhost:9002/ [Mon Oct 22 12:36:16 2007] [error] [client
127.0.0.1] Premature end of script headers: martview, referer:
http://localhost:9002/ [Mon Oct 22 12:36:33 2007] [error] [client 127.0.0.1]
(2)No such file or directory: exec of
'/var/biomart/biomart-0.6/biomart-perl/cgi-bin/martview' failed, referer:
http://localhost:9002/ [Mon Oct 22 12:36:33 2007] [error] [client 127.0.0.1]
Premature end of script headers: martview, referer: http://localhost:9002/ [Mon
Oct 22 13:41:15 2007] [notice] caught SIGTERM, shutting down [Mon Oct 22
13:50:44 2007] [notice] Apache/2.2.4 (Unix) !
