diff --git a/README.md b/README.md index e08042e..571b294 100644 --- a/README.md +++ b/README.md @@ -5,14 +5,51 @@ Welcome to kleEpistasis. A tool for performing 3-way genetic interaction analysi Contact: stefan.kleeberger@gmail.com (Stefan Kleeberger, Programmer), bmm@psych.mpg.de (Prof. Dr. Bertram Mueller-Myhsok, Supervisor) Max Planck Institute of Psychiatry, Munich, 2015 -In order to perform brute-force statistical 3-way interaction tests on SNP data, you will have to provide your data in PLINK binary format and a Phenotype in PLINK alternate phenotype format. Please see "http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed" and "http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#pheno" for more information regarding file formats. +## Still in developement! +This tool recently reached the status of BETA. The core functionality is hereby given. If there is any interest in using this tool, I will continue adding features to it. If you are interested in working with this tool and need assistence, please leave me a note (email above). +## compilation & needed thechnologies -Flags: +- You will have to have at least a CUDA 2.0 capable device (if not 3.5 you need to change the Makefile from sm_35 to sm_20) +- ... the complete CUDA toolkit installed +- You need (at the moment) a greater amount of memory (for 5k SNPs & 1k Individuals, we needed ~ 20 GB) +- At least 8 cores +- Candidate SNPs or at least pre-selected SNPs. Genome-wide won't be feasable... yet. +- make changes in the _Makefile_ +- make changes in the helperzz/build.sh file +- located in the kleEpistasis directory, you can either run +`make` +or, +`./helperzz/build.sh` +which is as small script I wrote to create the needed filesystem structure and compile using multiple threads simultaniously +- The resulting binary will be located in bin/kleEpistasis +## Changes you may have do need in the _Makefile_ -REQUIRED +Please cusomize your Makefile as you need. You may want to change +(friendly reminder: in sh shells there must not be any whitespace between VARIABLE=VALUE) + + +- the location of your cuda compiler nvcc (line 5) +- change the compute capability according to your device (e.g. m_35 to sm_20, line 5) +- the location of your cuda library (line 6) +- add debugging flags "-g -G" to OPT (line 7) +- and anything you want to change, as long as you know what you are doing. + +## How should my data look like? +In order to perform brute-force statistical 3-way interaction tests on SNP data, you will have to provide your data in PLINK binary format and a Phenotype in PLINK alternate phenotype format. Please see + +- "http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed" + +and + +- "http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#pheno" +for more information regarding file formats. + + +## Flags: +### REQUIRED '-path [path]' Absolute or relative path to plink files in binary format (.bed .bim .fam) !>> without <