InstallLiftOver

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Installation Guide UCSC liftOver

(Installation Guide is a bit of an overstatement at the moment...)

Some useful links:

  1. Download binary: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
  2. Configuration files (known as chains), for example for hg19: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/
  3. Web interface: http://genome.ucsc.edu/cgi-bin/hgLiftOver/

Configuration file locations:

  1. Main liftOver configuration file: /opt/galaxy/prog/galaxy-2011-7-21/tool-data/liftOver.loc
  2. Chain configuration files (like hg18ToHg17.over.chain): /opt/galaxy/prog/galaxy-2011-7-21/tool-data/liftOver/*.over.chain