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 :
- 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
- 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
- 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:
[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: