How to make Galaxy link to a local installed UCSC database?
Hallo every one, I am new to Galaxy, I have a idea which maybe not new to people here. I work on arabidopsis. maybe you know that UCSC do not offer the genome assembly for plant. so i will install UCSC locally and built the genome assembly for arabidopsis. this work is half done now. I also installed Galaxy, if i understand correctly, Galaxy has the link to UCSC so the user can get data from UCSC. since what i interested is arabidopsis information, I hope Galaxy can retrive data form the locally installed UCSC in future. I do not know if it is possible to make this idea come ture.maybe some of you have done it. if yes, I am gratefully if you can tell me the how to get it. many thanks, Xue
xue dong wrote:
I also installed Galaxy, if i understand correctly, Galaxy has the link to UCSC so the user can get data from UCSC. since what i interested is arabidopsis information, I hope Galaxy can retrive data form the locally installed UCSC in future. I do not know if it is possible to make this idea come ture.maybe some of you have done it. if yes, I am gratefully if you can tell me the how to get it.
Hi Xue, Sorry for the long delay in response. This can be done by copying the existing UCSC tool config (tools/data_source/ucsc_tablebrowser.xml) and changing the url to your local url: <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> Then add this new copy of the tool config to your tool_conf.xml. --nate
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xue dong