GeneTools installation

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Read this first


  • GNU C++ compiler
  • GSL
  • Eigen
  • Samtools
  • zLib
  • R
  • Pcre


  • 1. Download requisite libraries and compile them. Bundled files are stored on the lab SVN: common_third_party_lib/ . Use ./ to unpack and compile the libraries. Remember to add the environment variables and LD_LIBRARY_PATH to your startup script (e.g. ~/.bashrc)
cd common_third_party_lib/
./ unpack all
./ compile all
  • 2. Run configure and compile

To compile on i386 Mac, use:

./configure CXX="g++ -arch i386"

System-wide variable setup

  • There are some files commonly used by GeneTools that you don't want to manually specify every time you run the program. You can set up their default paths by specifying them in a "gm.cfg" file in the directory where you perform your analysis. The configuration file has the following format in variable name - value pairs.

# var-name      value
reffile         /path_to_your_databases/ucsc/refGene.txt.25Nov2009
refseq.fa       /path_to_your_databases/wg/RefSeq25Nov2009.fa

NOTE: the name and value are tab-separated.
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