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 :
            <!-- 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:

  http://lists.bx.psu.edu/

Reply via email to