Thanks for your answer Jen,
This functonnality still doesn't work on my galaxy instance :( .
To test external data integration, I test with a public external site in
order to get help.
So I would like to integrate the following gff tab data from this distant
site : http://ftp.maizesequence.org/current/mirna/ZmB73_miRNA.gff (I will
try with my Genome Browser, once this step will be ok).

In universe_wsgi.ini file, I try to set the GALAXY_URL :
GALAXY_URL=http://ftp.maizesequence.org/current/mirna/ZmB73_miRNA.gff

I encountered this error : "TypeError: serve() got an unexpected keyword
argument 'GALAXY_URL' "

I'm a little bit confused about external data integration settings, could
you help me ?

Thanks,
ben


2011/7/26 Jennifer Jackson <j...@bx.psu.edu>

> Hello Ben,
>
> Were you able to get the set up working? This is an older thread, and maybe
> this was resolved already, but I wanted to double check that you got help if
> still needed.
>
> Just in case you didn't see it yet, our wiki has been moved, and this is
> the location of the set-up config for the Galaxy side:
> http://wiki.g2.bx.psu.edu/**Admin/FAQ#Connect_an_external_**
> datasource_to_Galaxy<http://wiki.g2.bx.psu.edu/Admin/FAQ#Connect_an_external_datasource_to_Galaxy>
>
> Take care,
>
> Jen
> Galaxy team
>
> On 6/28/11 5:16 AM, BM wrote:
>
>> Hi,
>> I am trying to set up the galaxy outgoing and incoming funtionalities
>> in GBROWSE and GALAXY to send data between these applications.
>>
>> I have local instances of GALAXY and GBROWSE and I wonder how should I
>> configure these.
>>
>> How this should look in the GBROWSE user interface (in the "share this
>> track" section) ?
>> How this should look in the GALAXY user interface ?
>>
>> My GBROWSE version : 2.38 and my GALAXY version :
>> galaxy-galaxy-central-**fd3391bcd903
>> Here the conf I set up :
>>
>> ------MY GALAXY SETTINGS------
>> I saw in a previous topic posted by nicki
>> (http://gmod.827538.n3.nabble.**com/Send-data-to-GBrowse-**td2446346.html<http://gmod.827538.n3.nabble.com/Send-data-to-GBrowse-td2446346.html>
>> )
>> that some files must be edtited :
>>
>> 1. universe_wsgi.ini
>> I edited it as follows :
>> GBrowse servers: tool-data/shared/gbrowse/**gbrowse_build_sites.txt
>> gbrowse_display_sites =
>> wormbase,tair,modencode_worm,**modencode_fly,yeast_sgd,perso
>>
>> 2. tool-data/shared/gbrowse/**gbrowse_build_sites.txt
>> I edited it as follows :
>> #perso
>> perso
>> http://my_host.com/Gbrowse/**cgi-bin/gbrowse_details/specie<http://my_host.com/Gbrowse/cgi-bin/gbrowse_details/specie>
>>      specie
>>
>> 3.  datatypes_conf.xml
>> I edited it as follows :
>>             <!-- line uncommented by ben-->
>>             <display file="gbrowse/gbrowse_gff.xml" inherit="True" />
>>             <!-- line uncommented by ben-->
>>             <display file="gbrowse/gbrowse_wig.xml" />
>>
>> I have got the following files in "display_applications/gbrowse/**" :
>> gbrowse_gff.xml
>> gbrowse_interval_as_bed.xml
>> gbrowse_wig.xml
>>
>> ------MY GBROWSE SETTINGS------
>> I have edited the general section of
>> "/var/www/GBROWSE/conf/specie.**conf" according to the documentation
>> http://gmod.org/wiki/GBrowse_**Configuration_HOWTO#Track_**
>> Sharing_Options<http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options>
>> :
>>
>> [GENERAL]
>> galaxy outgoing = http:/my_host.com:8080/tool_**
>> runner?tool_id=ncbi_blastn_**wrapper<http://my_host.com:8080/tool_runner?tool_id=ncbi_blastn_wrapper>
>> galaxy incoming = 
>> https://my_host.com/Gbrowse/**cgi-bin/gbgff<https://my_host.com/Gbrowse/cgi-bin/gbgff>
>> -------------
>> First, I would like to look for the outgoing functionality from
>> GBROWSE to GALAXY.
>> Then,  the incoming functionnality : from GALAXY to GBROWSE
>>
>> I hope someone can help me, I'm new to GALAXY.
>>
>> Thanks,
>> greetings
>>
>> Ben
>> ______________________________**_____________________________
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>
> --
> Jennifer Jackson
> http://usegalaxy.org/
> http://galaxyproject.org/
> ______________________________**_____________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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>
>  http://lists.bx.psu.edu/
>
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