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

Allan Kamau kamauallan at gmail.com
Mon Nov 12 08:12:03 GMT 2012


I am still struggling to view gbrowse served pages of my mine "abc".

I did manually include the lines below at the end of my installations
"gbrowse2/GBrowse.conf" file

[abc.conf]
description     = Test Mine
path            = abc.conf

But my attempts to go to
"http://myservername/gb2/gbrowse/abc/<http://pipeline01.cbrc.kaust.edu.sa/gb2/gbrowse/yeast/>"
were been redirected to the sites I had previously viewed "
http://myservername/gb2/gbrowse/yeast/<http://pipeline01.cbrc.kaust.edu.sa/gb2/gbrowse/yeast/>"
or "http://myservername/gb2/gbrowse/volvox/<http://pipeline01.cbrc.kaust.edu.sa/gb2/gbrowse/yeast/>
".


My "~/.intermine/abc.properties" file includes the lines

project.sitePrefix=/abc
gbrowse.database=gbrowse
gbrowse.database.adaptor=mysql
gbrowse.database.source=abc
gbrowse.database.host=localhost
gbrowse.database.user=intermine
gbrowse.database.password=yyyy
gbrowse.database.write.user=zzzz
gbrowse.database.write.password=aaaa


gbrowse.config.directory=/apps/gbrowse2
gbrowse.www.directory=/var/www/gbrowse2




On Sat, Nov 10, 2012 at 1:59 PM, Allan Kamau <kamauallan at gmail.com> wrote:

> 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.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ______________________________****_________________
>>>>> dev mailing list
>>>>> dev at intermine.org
>>>>> http://mail.intermine.org/cgi-****bin/mailman/listinfo/dev<http://mail.intermine.org/cgi-**bin/mailman/listinfo/dev>
>>>>> <htt**p://mail.intermine.org/cgi-**bin/mailman/listinfo/dev<http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>>>> >
>>>>>
>>>>>
>>>>
>>>
>>>
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>>
>
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