Re: [galaxy-dev] GALAXY-GBROWSE : setting up incoming/outcomming functionalities (sharing data)

[Daniel Blankenberg]

Hi Ben,

Adding a GBrowse server to a Galaxy instance is done loosely in two halves: 1.) 
sending data from Galaxy to GBrowse and 2.) getting data into Galaxy from 
GBrowse. 

1.) sending data to GBrowse
You look to be on the right track for this from your previous comments. Just 
make sure that the dataset you are trying to send to GBrowse has the "dbkey" 
set to one of the values (e.g. "specie")  that you specified in 
gbrowse_build_sites.txt

2.) To send data to Galaxy from your GBrowse instance, you will need to add a 
new tool xml (usually under the "Get Data" section). To start, you can take the 
file "GALAXY_ROOT/tools/data_source/fly_modencode.xml" and make a copy of it. 
In the copy, you can change the values (at the top) to point to your specific 
gbrowse instance, e.g.:

server
data_source.py $output 
$__app__.config.output_size_limit
http://gbrowse.site/fgb2/gbrowse/organism"; 
check_values="false"> 
go to Ben GBrowse server $GALAXY_URL


you should also set "dbkey" to be the same as the value ("specie") that you 
will want to use to send back to GBrowse and which will also be used to 
uniquely represent the genome build within Galaxy.

Then you will need to add the link to the tool.xml file to Galaxy's 
tool_conf.xml file, just the same as with any Galaxy tool. 

Also, don't put GALAXY_URL in the universe_wsgi.ini file:
> 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' "



Please let us know if we can provide additional assistance.

Thanks for using Galaxy,

Dan


On Aug 1, 2011, at 5:40 AM, B M wrote:

> 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 
> 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
> 
> 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)
> 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  specie
> 
> 3.  datatypes_conf.xml
> I edited it as follows :
> 
> 
> 
> 
> 
> 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:
> 
> [GENERAL]
> galaxy outgoing = 
> http:/my_host.com:8080/tool_runner?tool_id=ncbi_blastn_wrapper
> galaxy incoming = 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
> __

Re: [galaxy-dev] GALAXY-GBROWSE : setting up incoming/outcomming functionalities (sharing data)

[B M]

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 

> 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
>
> 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
>> )
>> 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
>>  specie
>>
>> 3.  datatypes_conf.xml
>> I edited it as follows :
>> 
>> 
>> 
>> 
>>
>> 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
>> :
>>
>> [GENERAL]
>> galaxy outgoing = http:/my_host.com:8080/tool_**
>> runner?tool_id=ncbi_blastn_**wrapper
>> galaxy incoming = 
>> 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
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>>
>
> --
> 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
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
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Re: [galaxy-dev] GALAXY-GBROWSE : setting up incoming/outcomming functionalities (sharing data)

[Jennifer Jackson]

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

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)
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  specie

3.  datatypes_conf.xml
I edited it as follows :
 
 
 
 

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:

[GENERAL]
galaxy outgoing = http:/my_host.com:8080/tool_runner?tool_id=ncbi_blastn_wrapper
galaxy incoming = 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/
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