Hi Ben, Adding a GBrowse server to a Galaxy instance is done loosely in two halves: 1.) sending data from Galaxy to GBrowse and 2.) getting data into Galaxy from GBrowse. 1.) sending data to GBrowse You look to be on the right track for this from your previous comments. Just make sure that the dataset you are trying to send to GBrowse has the "dbkey" set to one of the values (e.g. "specie") that you specified in gbrowse_build_sites.txt 2.) To send data to Galaxy from your GBrowse instance, you will need to add a new tool xml (usually under the "Get Data" section). To start, you can take the file "GALAXY_ROOT/tools/data_source/fly_modencode.xml" and make a copy of it. In the copy, you can change the values (at the top) to point to your specific gbrowse instance, e.g.: <tool name="Ben GBrowse" id="ben_gbrowse" tool_type="data_source"> <description>server</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://gbrowse.site/fgb2/gbrowse/organism" check_values="false"> <display>go to Ben GBrowse server $GALAXY_URL</display> </inputs> you should also set "dbkey" to be the same as the value ("specie") that you will want to use to send back to GBrowse and which will also be used to uniquely represent the genome build within Galaxy. Then you will need to add the link to the tool.xml file to Galaxy's tool_conf.xml file, just the same as with any Galaxy tool. Also, don't put GALAXY_URL in the universe_wsgi.ini file:
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' "
Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Aug 1, 2011, at 5:40 AM, B M wrote:
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
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 :
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:
-- 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:
___________________________________________________________ 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: