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

Julie Sullivan julie at flymine.org
Wed Nov 7 13:58:31 GMT 2012


Yes, exactly.

On 07/11/12 13:53, Allan Kamau wrote:
> 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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