Send data to GBrowse

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Send data to GBrowse

Liisa
Hi,
I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse.

I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species http://domain.ca/cgi-bin/gbrowse/species   species)
 
As well as universe_wsgi.ini (gbrowse_display_sites = species)

However I do not see a link in history items after I stop and start the server.

Is there something else I'm missing?

Thanks in advance for your help,
Liisa
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Re: Send data to GBrowse

nicki

Hi Liisa

When setting this up on our own local instance to get bigwig files to display in Gbrowse we edited:

1. universe_wsgi.ini
2. tool-data/shared/gbrowse/gbrowse_build_sites.txt
3.  datatypes_conf.xml

so that it includes

<display file="gbrowse/gbrowse_wig.xml" />

4. and in display_applications/gbrowse/ make sure you have the relevant xml files

eg gbrowse_wig.xml, gbrowse_bigwig.xml

Nicki Gray
MRC Molecular Haematology Unit


On 7 Feb 2011, at 19:03, Liisa Koski wrote:

Hi,
I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse.

I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species http://domain.ca/cgi-bin/gbrowse/species   species)
 
As well as universe_wsgi.ini (gbrowse_display_sites = species)

However I do not see a link in history items after I stop and start the server.

Is there something else I'm missing?

Thanks in advance for your help,
Liisa<ATT00001.txt>


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[hidden email]
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Nicki Gray
MRC Molecular Haematology Unit
Weatherall Institute of Molecular Medicine
John Radcliffe Hospital
Oxford, UK, OX3 9DS
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Re: Send data to GBrowse

Liisa
I have figured out how to send data from my local Galaxy to my local GBrowse. Thanks for the help!

Now I would also like to go in the other direction and send data from GBrowse to Galaxy.

galaxy incoming = http://localhost/cgi-bin/gbrowse

When I export data to Galaxy I get the main page of galaxy but do not see any data.
The url in my browser is http://localhost:8080/?URL=http://localhost/cgi-bin/gbrowse

Any ideas as to why I can't see the actual data? Shoudn't the url contain ref;start;end;type?

Thanks for your help,
Liisa
 


From: Nicki Gray <[hidden email]>
To: Liisa Koski <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Date: 2011-02-10 11:40
Subject: Re: [galaxy-dev] Send data to GBrowse






Hi Liisa

When setting this up on our own local instance to get bigwig files to display in Gbrowse we edited:

1. universe_wsgi.ini
2. tool-data/shared/gbrowse/gbrowse_build_sites.txt
3.  datatypes_conf.xml

so that it includes

<display file="gbrowse/gbrowse_wig.xml" />

4. and in display_applications/gbrowse/ make sure you have the relevant xml files

eg gbrowse_wig.xml, gbrowse_bigwig.xml

Nicki Gray
MRC Molecular Haematology Unit


On 7 Feb 2011, at 19:03, Liisa Koski wrote:

Hi,
I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse.


I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species
http://domain.ca/cgi-bin/gbrowse/species   species)
 
As well as universe_wsgi.ini (gbrowse_display_sites = species)


However I do not see a link in history items after I stop and start the server.


Is there something else I'm missing?


Thanks in advance for your help,

Liisa
<ATT00001.txt>


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