Thanks Allan, as suspected, no signs of mode_perl configuration directives in your httpd.conf. However I would still need to look at your onscreen response when you run the following script.
perl bin/configure.pl -r con/your_registry_File.xml --clean In addition, you may consult Docs to find out how to configure mod_perl with apache. Having both configured is required for BioMart. Cheers syed On Mon, 2007-10-22 at 14:26 +0200, allank wrote: > 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) ! configured -- resuming normal operations [Mon Oct 22 13:56:05 2007] [notice] caught SIGTERM, shutting down [Mon Oct 22 13:56:10 2007] [notice] Apache/2.2.4 (Unix) configured -- resuming normal operations [Mon Oct 22 13:56:18 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 13:56:18 2007] [error] [client 127.0.0.1] Premature end of script headers: martview, referer: http://localhost:9002/ [Mon Oct 22 14:05:48 2007] [notice] caught SIGTERM, shutting down [Mon Oct 22 14:05:52 2007] [notice] Apache/2.2.4 (Unix) configured -- resuming normal operations [Mon Oct 22 14:06:12 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 14:06:12 2007] [error] [client 127.0.0.1] Premature end of script headers: martview, referer: http://l! ocalhost:9002/ [Mon Oct 22 14:06:51 2007] [notice] caught SIGTERM, shu t /2.2.4 (Unix) configured -- resuming normal operations [Mon Oct 22 14:07:25 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 14:07:25 2007] [error] [client 127.0.0.1] Premature end of script headers: martview, referer: http://localhost:9002/ -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
