[InterMine Dev] Unable to configure Intermine to work with GBrowse

Allan Kamau kamauallan at gmail.com
Wed Nov 7 13:53:44 GMT 2012


Thank you Julie, we did copy the gbrowse directory from FlyMine and them
made changes to the build.xml, project.properties and FlyMine.conf we then
renamed FlyMine.conf to <my_mine>.conf.
Now I am stuck at the section "Installing the flymine.conf file" of "
http://intermine.org/wiki/GBrowseConfiguration" document. Where it says
"First make sure that these two properties are in your
flymine-gbrowse.properties file:

  gbrowse.config.directory=/etc/apache2/gbrowse.conf
  gbrowse.www.directory=/var/www/gbrowse
"

I did not find the flymine-gbrowse.properties file under FlyMine directory,
perhaps the above entries should be in my ~/.intermine/<my_mine>.properties
file?

Allan.



On Wed, Nov 7, 2012 at 4:37 PM, Julie Sullivan <julie at flymine.org> wrote:

> Can you try to copy the /gbrowse directory from FlyMine? You'll have to
> replace "FlyMine" with your mine - in the build.xml, project.properties and
> FlyMine.conf.
>
> The script to create your new mine should have created this for you. But
> didn't. Sorry, I'll see that's fixed.
>
>
> On 07/11/12 07:59, Allan Kamau wrote:
>
>> I am using the documentation at "
>> http://intermine.org/wiki/**GBrowseConfiguration<http://intermine.org/wiki/GBrowseConfiguration>"
>> describing how to get
>> GBrowse to display data from Intermine.
>>
>> I have successfully installed GBrowse and can run and reconfigure the test
>> project "volvox". And I do have a fully functional mine running on
>> Intermine.
>>
>> I am stuck at the "Creating files for GBrowse" section. The instruction
>> "On
>> your local machine, in<mine>/gbrowse ..
>> I do not have gbrowse directory in my mine. Using my mine's directory as
>> my
>> current working directory, a search for the string (ant task)
>> "install-gbrowse-conf" exists only in build.xml found in
>> "../imbuild/gbrowse.xml" (relative to my mine's directory) and "write-gff"
>> ant task is found at "../imbuild/gbrowse.xml".
>>
>> What should I do to have my mine's directory furnished with files (and
>> directories) required to run the Intermine-GBrowse configuration exercise?
>>
>> Allan.
>>
>>
>>
>>
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>>
>
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