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
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>
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 nicki.gray@imm.ox.ac.uk To: Liisa Koski liisa.koski@dnalandmarks.ca Cc: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu 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>
galaxy-dev@lists.galaxyproject.org