The pipeline requires 5 third party software (see the third party folder): CD-HIT, meme suite, SEECER, razers3 and velvet They aready have compiled version in the third-party folder, if the compiled binary file does not work in your platform, use the following steps to recompile:

1. Compile SEECER Requirements: SeqAn, GNU Scientific Library cd SEECER-0.2/ cd jellyfish-1.1.4/ ./configure make cd .. cd SEECER/ ./configure make

2. Compile velvet cd velvet make

3. Compile meme tar zxf meme_4.9.0_4.tar.gz cd meme_4.9.0/ ./configure --prefix=${software_home_directory}/third-party/meme --with-url="http://meme.nbcr.net/meme" make make test make install (Here ${software_home_directory} is the home directory of software package)

4. Compile CD-HIT cd cd-hit-v4.6.1/ make

5. Compile RazerS3 cd seqan-trunk/ mkdir build/Debug cd build/Debug cmake ../.. -DCMAKE_BUILD_TYPE=Debug make test_basic ./core/tests/basic/test_basic

To run this program, after it has been installed using the user guide above (or using the already compiled version) you should first move to the script directory and run the program as: ./pipeline.sh <list of motif databases (separated with ":")> <"1" to use SEECER, "0" for velvet> Before running the program, you should first change the config.sh file to change ROOTDIR into home directory of this software package.