Interfacing Galaxy With A Local Copy Of The Ucsc Genome Browser

Question: Interfacing Galaxy With A Local Copy Of The Ucsc Genome Browser

10.4 years ago by

Tim Yu • 20

Tim Yu • 20 wrote:

hi there, We've just set up a local instance of Galaxy to serve as a framework for adding custom tools. We also have a local server running a copy of the UCSC genome browser with our own data on it. Is there a way to configure Galaxy to interface with our in-house UCSC server, instead of (or in addition to) the central site? Is this, by the way, the approved place to direct such questions? I didn't see an email address for support on the main site or wiki. Thanks! Tim Yu

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modified 10.4 years ago by Greg Von Kuster • 840 • written 10.4 years ago by Tim Yu • 20

10.4 years ago by

Greg Von Kuster • 840

Greg Von Kuster • 840 wrote:

Hello Tim, Details about connecting to external data sources can be found in our DataSources wiki at http://g2.trac.bx.psu.edu/wiki/DataSources To keep the connection to the UCSC genome browser that comes with the Galaxy distribution, make a copy of the tool config in ~/tools/data_source/ucsc_tablebrowser.xml, naming it to something related to your local instance ( or you could simply change the following tag information if you choose ). The following information should be changed to point to your local instance, specifically the url in the inputs action. ucsc_tablebrowser.py $output <inputs action="<a href=" http:="" genome.ucsc.edu="" cgi-bin="" hgTables"="" rel="nofollow">http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> <display>go to UCSC Table Browser $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner"/> <param name="tool_id" type="hidden" value="ucsc_table_direct1"/> <param name="sendToGalaxy" type="hidden" value="1"/> <param name="hgta_compressType" type="hidden" value="none"/> <param name="hgta_outputType" type="hidden" value="bed"/> </inputs> If you copy this tool, you'll want to also copy the "ucsc_tablebrowser.py" and "ucsc_tablebrowser_code.py" executables, naming them appropriately. You'll also need to add the new tool to the "Get Data" tag set of your tool_conf.xml file with a new tag similar to this: <tool file="data_source/<your_local>_tablebrowser.xml"/> This is fine. You should also subscribe to the galaxy-dev@bx.psu.edu email list so tha tyou can receive messages for all of the new mercurial / svn code repository commits - we are continually enhancing the Galaxy distribution with new features/ fixes, etc. Greg Von Kuster Galaxy Development Team

ADD COMMENT • link written 10.4 years ago by Greg Von Kuster • 840

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