#A PLINK-based implementation of the "ESM" test for associations due to rare alleles in GWAS data
Implements an association test based on the ESM statistic first desribed here and published here.
- [GCC] (https://gcc.gnu.org/gcc-4.8/) -- version 4.8+
- PLINK! -- 1.90a was used, but 1.07 also works.
- boost -- Version 1.53 or greater is fine.
- zlib -- Version 1.2.7 is required. mergeperms.cc checks this at compile time and will fail if a lower version number is encountered
- GSL
- HDF5 -- version 1.8.11 or greater is fine (Install with --enable-cxx during configure step)
- Python--2.7.2+ with numpy and h5py -- Only needed if using h5merge.py,which is not strictly necessary
Please use your system's package installation tools to install the above whenever possible.
##Installing ESM
git clone https://github.com/ThorntonLab/ESMtest.git ESMtest
cd ESMtest
./configure
make
make install
If you want to install it in non-standard location (i.e your prefix if not /usr/local/) then:
cd ESMtest
./configure --prefix=$HOME (or wherever you want it to go)
make
make install
We have found an issue with installation on Ubuntu 15. HDF5. There are separate serial and MPI versions of HDF5. Most likely you hhave the serial version installed. Thus you will need to be more specific about the headers and runtime libraries.
We recommend that you symlink the preferred library to the regular name, so that it can be linked with -lhdf5. Perhaps your libhdf5_serial.so is in '/usr/lib/x86_64-linux-gnu'
link ~/lib/libhdf5.so /PATH/TO/libhdf5_serial.so
Add the path to LDFLAGS.
LDFLAGS=-L$HOME/lib
You will also need specify the directory of the HDF5 header files:
CPPFLAGS=-I/usr/include/hdf5/serial