Hi Nelson, You definitely should not need to touch apache's httpd.conf file at all and it will be fine to run the reactome website and BioMart off the same apache unless performance becomes an issue. Put the httpd.conf file back how it was and instead edit conf/settings.conf in the biomart-perl directory to change the port from 80 to some other port but it sounds like you may have already changed it to 9002?
Anyhow for now, once you have reinstated your httpd.conf file in the biomart-perl directory do the following and let is know what errors you get: (i) from the biomart-perl directory kill `cat logs/httpd.pid` (ii) perl bin/configure.pl --clean -r conf/martReg.xml replacing the martReg.xml with whatever your registry is called (iii) /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd -d $PWD -f /homes/nndegwa/biomart-perl/conf/httpd.conf replacing the argument to -f with wherever your biomart-perl install is. You should be using the biomart-perl httpd.conf. Below you were using the one in your apache install. (iv) if working point your browser to localhost:9002/biomart/martview Let us know how that goes. Cheers Damian On Tue, Mar 23, 2010 at 4:51 AM, <[email protected]> wrote: > Hi All, > Firstly, i would like to thank all who took their time and offered really > helpful suggestions to troubleshoot my task of installing Biomart 0.7 on > 64 bit linux. > May i mention that as i do not have root access to the machine am using, i > installed my own - lets say most of the things (64 bit perl, apache, the > works, edited .bashrc file to point to my installed perl and updated the > required modules via cpan) > I have made some progress so far: > I have my local reactome website up and running - Biomart:query, link is > my main worry. > Successfully completed configuring MartView (section 1.4.3.2) > I was able to start Martview (didn't attempt to stop it) - however a few > interesting things happened here - so here i am with more questions > > NB: Both the reactome website (mostly written in perl) and Biomart are > sharing the same Perl and apache i installed - not sure how bad this is. > The first time i attempted to configure martview as shown below, i got the > error shown > > [my_shell]$/homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd > -d $PWD -f > /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/conf/httpd.conf > > The error that comes up is: > (13)Permission denied: make_sock: could not bind to address 0.0.0.0:80 > no listening sockets available, shutting down > Unable to open logs > > I went ahead to edit httpd.conf file by commenting out the 'Listen 80' to > '#Listen 80'. Now i get the following different error from previous above > when i attempt to configure martview as in 2.4.4: > > [my_shell]$ /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd > -d $PWD -f > /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/conf/httpd.conf > no listening sockets available, shutting down > Unable to open logs > > So i threw in some arbitrary port number 'Listen 5555' > and repeated the same command and this time round there was no more > complaints. > > The following 'http://localhost:5555/' on my browser yields a bold "It > works!" statement but 'http://localhost:5555/biomart/martview' says > something else: > '404 Not Found > The requested URL /biomart/martview was not found on this server.' > > Another interesting thing is that 'http://localhost:9002/' on the browser > brings up a nice logo and some info and a link to start Martview session > " > BioMart logo version 0.7 > > Start BioMart BioMart is a generic data management system which offers a > range of advanced query interfaces and administration tools..... > > Start MartView session > " > When i click this link however i get the following error: > > "Internal Server Error > > The server encountered an internal error or misconfiguration and was > unable to complete your request. > > Please contact the server administrator, [no address given] and inform > them of the time the error occurred, and anything you might have done that > may have caused the error. > > More information about this error may be available in the server error > log." > > So i head back to the biomart-perl/logs and the errors given are many, as > shown below, i however tried to first rule out any require module errors > by getting those modules required via cpan and the only one i did actually > install was Time::HiRes, the rest according to CPAN were existing and up > to date. In spite of this effort, the error logs remained exactly the > same. > > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] DynaLoader object > version 1.08 does not match $DynaLoader::XS_VERSION 1.0802 at > /homes/nndegwa/reactomes/Reactome/test/perl64/lib/DynaLoader.pm line 92., > referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Time/HiRes.pm line > 7., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Util/TimeTracker.pm > line 19., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN > failed--compilation aborted at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Util/TimeTracker.pm > line 22., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout/PatternLayout.pm > line 14., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN > failed--compilation aborted at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout/PatternLayout.pm > line 14., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout.pm > line 5., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN > failed--compilation aborted at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout.pm > line 5., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Logger.pm > line 11., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN > failed--compilation aborted at > > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Logger.pm > line 11., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl.pm > line 12., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN > failed--compilation aborted at > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl.pm > line 12., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed > in require at > > /automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/cgi-bin/martview > line 43., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN > failed--compilation aborted at > > /automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/cgi-bin/martview > line 43., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Undefined subroutine > &Log::Log4perl::Logger::cleanup called at > /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl.pm > line 5., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] END failed--call > queue aborted at > > /automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/cgi-bin/martview > line 43., referer: http://localhost:9002/ > [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Premature end of > script headers: martview, referer: http://localhost:9002/ > > This is the furthest i have got and would greatly appreciate your > assistance. Thank you > Kind Regards, > Nelson > > PS: Sorry for the lengthy message, i hope it reveals the minimum > information needed to troubleshoot. > > > > [email protected] wrote: > >> Hi James, > >> I tried out Leandro's suggestion and still got the same error. > >> I have notified him to see if he perhaps might offer some other > >> suggestions. > >> I would also like to know how you guys got round this issue - i would > >> really appreciate. > Thanks > >> Nelson > >> > >> > >> > > Comment out "use CGI::Session::Driver::db_file;" in the BioMart::Web > > module! > >>> Leandro Hermida wrote: > >>> > >>>> Hi, > >>>> > >>>> Sorry to chime in in the middle, something is up with your Perl. > >>>> Using the same Perl that have used to build your BioMart and run the > >>>> BioMart configure script, try the following: > >>>> > >>>> perl -e 'use DB_File;' > >>>> or > >>>> perl -MDB_File > >>>> > >>>> do you get the same error? > >>>> > >>> Ensembl got round this issue by commenting the line out the use DB_File > >>> in the mart code (along with a number of other tweaks we make) to > >>> remove > >>> this necessity - as we use MySQL sessions anyway. > >>> > >>> > >>> > >> > >> > >> > > > > > > >
