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

Allan Kamau kamauallan at gmail.com
Sat Nov 10 10:59:14 GMT 2012


I have successfully performed the steps outlined in the Intermine+GBrowse
document "http://intermine.org/wiki/GBrowseConfiguration" but I am unable
to determine the URL by which to access my mine's GBrowse powered pages.
Assuming my mine name is "abc" and my GBrowse example application "yeast"
is accessible at
"http://myservername/gb2/gbrowse/yeast/<http://pipeline01.cbrc.kaust.edu.sa/gb2/gbrowse/yeast/>"
could my mine's ("abc") the GBrowse driven pages be at "
http://myservername/gb2/gbrowse/abc/<http://pipeline01.cbrc.kaust.edu.sa/gb2/gbrowse/yeast/>"
I
have tried this link but I keep getting redirected (automatically) to "
http://myservername/gb2/gbrowse/yeast/<http://pipeline01.cbrc.kaust.edu.sa/gb2/gbrowse/yeast/>
".

Allan.


On Wed, Nov 7, 2012 at 4:58 PM, Julie Sullivan <julie at flymine.org> wrote:

> 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<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>
>>>> <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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>
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