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
[s...@sans-lab-04 biomart-perl]$ perl bin/configure.pl -r
conf/registryURLPointer.xml
Do you want to install in API only mode [y/n] [n]: y
API configure only checks dependencies for using API
Any additional switches supplied to this script will be ignored
Checking prerequisites ...
Looks good.... you are done.
[s...@sans-lab-04 biomart-perl]$ perl bin/configure.pl -r
conf/registryURLPointer.xml
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
Use of uninitialized value in scalar assignment at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/List/MoreUtils.pm
line 31.
APACHE: /local/biomart/apache/bin/httpd
HOST: localhost
PORT: 80
PROXY:
LOCATION: biomart
APXS/2:
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /local/biomart/apache/bin/httpd, probing for version &
ModPerl configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl
in httpd.conf.
Libdir /local/biomart/biomart-perl/lib is not in @INC, adding to @INC
Processing Cached Registry:
/local/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached
