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Thanks for this info. I'll see if I can add it to the docs for the 0.6
release.
cheers,
Richard
Eric wrote:
> 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:
>
> 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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