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 <jen@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 ______________________________**_____________________________ 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:
-- 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: