Use With Local Browser Mirror

Question: Use With Local Browser Mirror

10.7 years ago by

Keith Lamont • 10

Keith Lamont • 10 wrote:

Hi all, Is it possible to customize Galaxy to use a mirror of the genome browser? Thanks, Keith Lamont

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modified 10.7 years ago by James Taylor • 320 • written 10.7 years ago by Keith Lamont • 10

10.7 years ago by

James Taylor • 320

United States

James Taylor • 320 wrote:

Keith, For getting data, the easiest thing to do is to create a new tool config. Copy "tools/data_source/ucsc_tablebrowser.xml" in your Galaxy instance to something like "tools/data_source/ ucsc_tablebrowser_local_mirror.xml". Then in that file change (1) the name and id attributes of the <tool> element to something unique and (2) the action attribute of the <inputs> element to point to the URL of your mirror. Then add the new tool config to your "tool_conf.xml". As long as your UCSC mirror is a reasonably recent version, it will then communicate properly with your local Galaxy instance. Please let us know if you have any problems. Thanks, James

ADD COMMENT • link written 10.7 years ago by James Taylor • 320

10.7 years ago by

James Taylor • 320

United States

James Taylor • 320 wrote:

Keith, Also, if you are interested in being able to display datasets in your local browser mirror, you can modify the file "static/ucsc/ ucsc_build_sites.txt". You will need a line like: site_name http://URL build1,build2,build3... The third field is the list of builds supported by that site, you can likely just copy the line for "main", or modify the list if you have a partial mirror. You will also need to add "site_name" to "ucsc_display_sites" in universe_wsgi.ini Thanks, James

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