Thanks for the help. This morning while duplicating my process in order to
provide good documentation I managed to make it work. Amazing how often
things work better after a good nights sleep.
In the event anyone is interested here is my procedure for making biomart
work on OS 10.4
Today I will attempt to get biomart to work with my own dataset
My procedure for installing biomart on OS 10.4:
1) download release-0_5 biomart-perl from cvs
2) cpan install prerequisite perl modules
3) download, configure, make and install apache 2.2.4 (w/ --enable-defalte
and --prefix-/usr/local/apache)
4) from /usr/local/biomart (my install site). "perl bin/configure -r
/conf/registryURLPointer.xml"
5) start apache ("/usr/local/apache/bin/httpd -d /usr/local/biomart -f
/usr/local/biomart/conf/httpd.conf
Error 1: Useless use of AllowOverride on lines 36,44,61,70
I figured this was an apache version issue so I deleted the offending lines.
Overrides wouldn't seem to matter when the web server is used only for
biomart.
Error 2: Couldn't determine Username.
This seems to be an OS X error with apache defaults. I added "User www" to
the top of the httpd.conf file and restart apache. (I also changed the
ownership of the biomart directory to "www")
Error 3: no such file or directory (apache starts, but this is in the log)
Martview, martresults and martservice can't find perl. I modify the first
line of each script to my perl location (#!/usr/bin/perl)
Error 4: When I run martview I get the following error in my web browser.
ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
"settingsParams" on an undefined value at
/usr/local/biomart/lib/BioMart/Web.pm line 116.
And
Exception::Class::Base::new /usr/local/biomart/cgi-bin/martview:79
constantine:/usr/local/biomart/logs root#
I thought there might be a mod_perl problem so I installed mod_perl from
source and reconfigured biomart with the --clean option
This seems to work. I added back the AllowOverride lines. It generates
warnings, but still seems to work.
I think that my fundamental problems were a problem with my biomart install
seeing my fink installed mod_perl and not using --clean when reconfiguring.
Thanks
On 5/1/07 3:20 AM, "Richard Holland" <[EMAIL PROTECTED]> wrote:
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> Could you send us the httpd.conf file that was generated so that we can
> see if we can spot any patterns.
>
> Also, what was the command you typed to start Apache, and what is the
> current working directory you are in when you type it?
>
> cheers,
> Richard
>
>
> Eric Ross wrote:
>> I'm not having much luck getting biomart to install on an OS X Xserve.
>> The compilation works without a hitch and I am able to configure with
>> one of the stock .xml files (perl bin/configure.pl -r
>> conf/registryDBPointer.xml )
>>
>> But when I start apache it complains
>> "Invalid command '/usr/local/biomart-perl/conf/registryDBPointer.xml',"
>>
>> The configure script seems to just add the file name to the top of the
>> httpd.conf file and apache chokes on it.
>>
>> Does anyone have suggestions?
>>
>> Thanks,
>>
>> Eric
>>
>>
>>
>>
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--
Eric Ross
Alejandro Sánchez Lab
Howard Hughes Medical Institute
Department of Neurobiology and Anatomy
University of Utah
Wintrobe 531
[EMAIL PROTECTED]
801-585-3674
