Thanks Syed, I created a new user and added it manually to httpd.conf. Everything works fine now.
Thanks again, Liisa Koski Bioinformatics Programmer T: (450)358-2621 x104 DNA Landmarks Inc. 84 Richelieu St.-Jean-sur-Richelieu, J3B 6X3 Quebec, Canada [EMAIL PROTECTED] Syed Haider <[EMAIL PROTECTED]> 2008-10-10 11:14 To Liisa Koski <[EMAIL PROTECTED]>, mart-dev <[email protected]> cc Subject Re: [mart-dev] Problems starting Mart View Hi Liisa, your apache is not started correctly. Please see the user directive exception in error_log. You need to add the user directive in conf/httpd.conf manually after perl bin/configure.pl step. Please dont forget that this file gets recreated every time you reconfigure, therefore you need to manually add the apache user directive in httpd.conf again. once done, kill existing apache and restart it. Should work afterwards. Good luck! syed On Fri, 2008-10-10 at 11:00 -0400, Liisa Koski wrote: > > > > > > Thanks Syed! > > > Liisa Koski > Bioinformatics Programmer > > T: (450)358-2621 x104 > DNA Landmarks Inc. > 84 Richelieu > St.-Jean-sur-Richelieu, J3B 6X3 > Quebec, Canada > [EMAIL PROTECTED] > > > Syed Haider <[EMAIL PROTECTED]> > > 2008-10-10 10:47 > > > To > Liisa Koski > <[EMAIL PROTECTED]> > cc > [email protected] > Subject > Re: [mart-dev] > Problems starting > Mart View > > > > > > > > > > Hi Liisa, > > Could you please send me the following: > > - conf/httpd.conf > > - logs/error_log > > thanks syed > > > On Fri, 2008-10-10 at 10:16 -0400, Liisa Koski wrote: > > > > Hi, > > I have used MartBuilder and MartEditor to build and configure a > mart. > > I have two questions. > > 1. When I choose Export from the MartEditor File menu to save the > > configuration nothing happens. Is the configuration saved somewhere > > automatically or should I be asked where? > > > > 2. I created myRegistry.xml in the biomart-perl/conf directory and > ran > > perl bin/configure.pl -r conf/myRegistry.xml. I am not asked any > > questions at this step and the output looks like > > > > Got usable Apache in /usr/local/apache-2.2.8/bin/httpd, probing for > > version & ModPerl configuration > > Have Apache DSO-support and ModPerl library file present, > configuring > > ModPerl in httpd.conf. > > Libdir /usr/local/biomart-perl/lib is not in @INC, adding to @INC > > > > > > > > Connection parameters of [test_maize_mart] [ OK ] > > > > > > [NEW CONFIGURATION] .... WITH MEMORY [default] > > default ... test_maize_mart .......... 001/001 ... > > gene_stable_id ............................ (RDBMS) > > localhost:3306 ................ OK > > Setting possible links between datasets > > ....(scanning) 100% > > ....(linking) 100% > > ....(sorting) 100% > > ....(clustering) 1/1 - 0 remain > > ....(resolving) 100% > > Building templates for visible datasets > > .... 100% > > Compiling templates for visible datasets > > [1/1] Attribute Panel of Dataset.. :gene_stable_id > > [1/1] Filter Panel of Dataset..... :gene_stable_id > > > > > > I start MartView by typing /usr/bin/httpd -d $PWD > > > > In the web browser I can type http://localhost:port and see the > > BioMart Project Page but if I add /biomart/martview I get a 500 > > Internal Server Error. > > > > > > Thanks in advance for your help, > > > > Liisa > > > > > > > -- > ====================================== > 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. ======================================
