Thanks for the quick response!
please refer to docs or you may see the quick install guide
(http://www.biomart.org/install-overview.html) about how to set your
conf/settings.conf which contains useful information about your apache
binary , host, port etc etc.
Right. I'm following those instructions, but I was sort of expecting to
see "Looks good.... you are done." at the end of step 1.3.4.1. It does
say "Configuration of the Perl API requires a single step". If any of
you guys are involved in this guide, may I suggest adding a few words
along the lines of "if you experience difficulties, please see section
X.Y on how to configure Z"?
As you can see in your install attempt, it cant find apache binary and
subsequently fails on mod_perl and other libraries.
Check. Fixed it for my platform. It's called apache2 on debian/ubuntu
systems. Now I have this error message instead:
$ 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 string ne at /media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl line 84.
Use of uninitialized value in regexp compilation at
/media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl line
86.
rm
/media/sda8/yohell/download/biomart/biomart-perl/conf/templates/default/*.ttcrm:
cannot remove
`/media/sda8/yohell/download/biomart/biomart-perl/conf/templates/default/*.ttc':
No such file or directory
APACHE: /usr/sbin/apache2
HOST: localhost
PORT: 9002
PROXY:
LOCATION: biomart
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl
configuration
Can't exec "/usr/sbin/apxs2": No such file or directory at
/media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl line 147.
Use of uninitialized value in scalar chomp at
/media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl line
148.
Use of uninitialized value in concatenation (.) or string at
/media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl line
150.
Libdir /media/sda8/yohell/download/biomart/biomart-perl/lib is not in @INC,
adding to @INC
Processing Cached Registry:
/media/sda8/yohell/download/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached
(what's all that "use of uninitialized value" business? It doesn't look
too good, does it?)
Any suggestions?
/Joel
