PhylEx: Integrated analysis of bulk and single cell RNA-seq

This software performs integrated analysis of bulk DNA-seq and single cell RNA-seq data.

Requirements

Recommended approach is to install homebrew package manager for OSX.

brew install cmake
brew install pkg-config
brew install gsl
brew install boost
brew install libomp

On most compute clouds requirements can be satisfied by loading the modules. For example

module load gsl
module load cmake
module load boost
module load openmpi
module load gcc

To compile the code, it is first required to initialize eigen submodule:

git submodule init
git submodule update

To build:

mkdir build
cd build
cmake ..
make install

This will create run, simul and testing executables. To run:

./run -c <config_file>

An example of the configuration file is provided in a separate repository for analysis here.

Note 1: this will install libtssb.a library file in your local/bin directory unless you specify it with the cmake command option

cmake -DCMAKE_INSTALL_PREFIX=$HOME/opt ../src

Note 2: there seems to be an issue with ABI, especially with regards to the compilation of the boost library on a computer cloud.

Adding the following line

add_compile_definitions(_GLIBCXX_USE_CXX11_ABI=0)

to CMakeLists.txt seemed to do the trick. Set to 1 or remove the line if any problem is encountered.

Alternatively, installing the latest version of the boost library may solve the problem as per this issue.