This software performs integrated analysis of bulk DNA-seq and single cell RNA-seq data.
gsl
boost
cmake
libomp
pkg-config
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.