diff --git a/README.md b/README.md index 475e9a7..5d77737 100644 --- a/README.md +++ b/README.md @@ -7,17 +7,21 @@ Contact: [Stefan Kleeberger](mailto:stefan.kleeberger@gmail.com) (Programmer), ## Still in development! -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 assistance, please leave [me a note](mailto:stefan.kleeberger@gmail.com) (email above). +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 assistance, please leave [me a note](mailto:stefan.kleeberger@gmail.com). ## Compilation & needed technologies -- 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) + +#### Prerequisites +- 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 5000 SNPs & 1000 Individuals, we needed ~20 GB) - At least 8 cores + +#### Preparations - Candidate SNPs or at least pre-selected SNPs. Genome-wide won't be feasible ... yet. -- make changes in the _Makefile_ -- make changes in the _helperzz/build.sh_ file +- make appropriate changes in the _Makefile_ (see below) +- make appropriate changes in the _helperzz/build.sh_ file - located in the kleEpistasis directory, you can either run `make` or, @@ -28,11 +32,11 @@ which is a small script to create the needed filesystem structure and compile us ## Changes you may need to make in the _Makefile_ Please customize your Makefile as you need. You may want to change -(friendly reminder: in sh shells there must not be any whitespace in `VARIABLE=VALUE`) +(friendly reminder: in `sh` shells there must not be any whitespace in `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) +- 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 else you want to change, as long as you know what you are doing.