Hi Sri, The error below means that the mod_perl library was not installed in your Perl's @INC.
During the mod_perl makemaker step in the BioMart docs: perl Makefile.PL \ PREFIX=/home/biomart/apache \ MP_APXS=/home/biomart/apache/bin/apxs it will put the mod_perl library files in the default location which is in that Apache's lib directory, /home/biomart/apache/lib for the example above. You will see it is putting them there at the make install step where it has many lines saying "Installing ...". Apache's lib directory is not in your Perl's @INC so you get this error you mentioned. So you can do one of two things: 1. Always start BioMart HTTPD setting PERL5LIB to Apache's lib dir before: PERL5LIB=/home/biomart/apache/lib /local/biomart/apache/bin/httpd -d $PWD/ -f $PWD/conf/httpd.conf. This will add this path to Perl's @INC 2. Or during the mod_perl makemaker step above tell it to put the mod_perl library files in the Perl's site_lib: perl Makefile.PL \ PREFIX=/home/biomart/apache \ MP_APXS=/home/biomart/apache/bin/apxs \ INSTALLSITELIB=/usr/lib64/perl5/site_perl/5.8.8 It will then put everything in /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi which is already in your @INC. For the second option for your installation looks like you would need superuser privileges. hth, Leandro On Wed, Dec 15, 2010 at 2:42 PM, Sri Krishna Suresh Kumar < sureshki...@gmail.com> wrote: > Hi Syed, > > Now I get this error > > I also tried as sudo. Still got the same error. Any suggestions? > > > [s...@sans-lab-04 biomart-perl]$ /local/biomart/apache/bin/httpd -d > $PWD/ -f $PWD/conf/httpd.conf > > Processing Cached Registry: > > /local/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached > > Syntax error on line 37 of /local/biomart/biomart-perl/conf/httpd.conf: > failed to resolve handler `Apache2::PerlSections': Can't locate > Apache2/PerlSections.pm in @INC (@INC contains: > /local/biomart/biomart-perl/lib > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl > /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 > . /local/biomart/biomart-perl/) at (eval 106) line 3.\n > > > > Thanks and Regards, > Sri Krishna > On Wed, Dec 15, 2010 at 1:28 PM, Syed Haider <syed.hai...@oicr.on.ca> > wrote: > > Of course, its a directory. You need to type this: > > > > /local/biomart/apache/bin/httpd -d $PWD/ -f $PWD/conf/httpd.conf > > > > > > > > Syed > > > > On 15/12/2010 12:18, Sri Krishna Suresh Kumar wrote: > >> > >> Hey Syed, > >> > >> I get this following error > >> > >> -bash: /local/biomart/apache/bin: is a directory > >> > >> Thanks and Regards, > >> Sri Krishna > >> > >> On Wed, Dec 15, 2010 at 1:23 PM, Syed Haider<syed.hai...@oicr.on.ca> > >> wrote: > >>> > >>> Hi Sri, > >>> > >>> please write what exactly is the ERROR, that would definitely help us. > >>> > >>> Syed > >>> > >>> On 15/12/2010 12:13, Sri Krishna Suresh Kumar wrote: > >>>> > >>>> Hi Leandro and Syed, > >>>> > >>>> Thanks a lot for the quick replies. My perl version is 5.8.8. I have > >>>> also attached the registryURLPointer file. > >>>> > >>>> The --clean option did the trick. Got this message in the end > >>>> "Compiling templates for visible datasets". > >>>> > >>>> Thanks a lot again. > >>>> > >>>> Could you kindly help me with the next step. > >>>> > >>>> In order to start and stop the mart view, the help document says I > have > >>>> to > >>>> type > >>>> > >>>> /my/chosen/Apache/binary -d $PWD -f $PWD/conf/httpd.conf > >>>> > >>>> So I try and type > >>>> > >>>> /local/biomart/apache/bin -d $pwd -f $pwd/conf/httpd.conf > >>>> > >>>> And I get an error message. I know I am doing something wrong here. > >>>> Could you tell me how to correct the mistake and start the mart view > >>>> correctly? > >>>> > >>>> Thanks and Regards, > >>>> Sri Krishna > >>>> On Wed, Dec 15, 2010 at 12:53 AM, Syed Haider<syed.hai...@oicr.on.ca> > >>>> wrote: > >>>>> > >>>>> Hi Sri, > >>>>> > >>>>> have you tried --clean option while you do perl bin/configure ? > >>>>> > >>>>> > >>>>> Syed > >>>>> > >>>>> On 14/12/2010 15:32, Sri Krishna Suresh Kumar wrote: > >>>>>> > >>>>>> Hello, > >>>>>> > >>>>>> I have been trying to install Biomart in my work system. > >>>>>> > >>>>>> I was able to install pre-requisites for biomart-perl using CPAN and > >>>>>> also completed the installation of Apache (2.2.17) and > >>>>>> mod-perl(2.0.4). > >>>>>> > >>>>>> I have also installed the Biomart-perl api (step 1.4.3.1) and I > >>>>>> recieved the message "Looks good... You are done". > >>>>>> > >>>>>> After this step, when I try to configure the MartView, after chaging > >>>>>> the setting.conf file and executing the command perl "bin/ > configure.pl > >>>>>> -r conf/registryURLPointer.xml" with the answer n to the subsequent > >>>>>> question, I did not get the message "Compiling templates for visible > >>>>>> datasets". Instead It stops prematurely with out any major error > >>>>>> outputs. However I see a warning message of use of uninitialised > >>>>>> variable in a CPAN module. I am attaching the file with the command > >>>>>> issued and the subsequent output received. > >>>>>> > >>>>>> Could you let me know if I am doing anything wrong? Or if this is > >>>>>> normal? > >>>>>> > >>>>>> Thanks and Regards, > >>>>>> Sri Krishna Suresh Kumar > >>>>> > >>> > > >
