GeneTools installation

From Icbwiki

Contents 1 Read this first 2 Requirements 3 installation 4 System-wide variable setup

Read this first

• The SVN repository is currently open only to internal users. But we have a precompiled version of GeneTools. Please email us to request a copy of the software.

Requirements

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

installation

• 1. Download requisite libraries and compile them. Bundled files are stored on the lab SVN: common_third_party_lib/ . Use ./install.sh 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/
./install.sh unpack all
./install.sh compile all

• 2. Run configure and compile

./configure
make

To compile on i386 Mac, use:

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

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.

E.g.

# 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.