Cross-species module discovery
C++ Python CMake
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README.md
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README.md

Software description

xHeinz is a software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions.

Active subnetwork modules are sets of genes, one for each species, which:

  • induce a connected subnetwork in a species-specific interaction network,
  • show overall differential behavior, and
  • contain a large number of orthologous genes.

Compilation instructions

Dependencies

  • Boost (>= 1.49)
  • LEMON 1.3
  • ILOG CPLEX (>= 12.0)
  • Compiler that supports C++11

Installation instruction for MacOS X 10.9 and 10.8.5

In Mavericks the default C++ standard library is libc++ instead of libstdc++. Since the CPLEX library is using libstdc++, we are forced to use this as well. However, the provided Clang compiler is not able to compile C++11 code when using libstdc++. That is why we resort to gcc 4.8.

To install gcc-4.8 via homebrew:

brew tap homebrew/versions
brew install gcc48

If an outdated version of brew is installed, this step will fail with the following error

 Error: undefined method `cxxstdlib_check' for gcc48:Gcc48

In which case the latest version of brew have to be installed :

brew update 

Note that brew update might fail with the following error

Error: undefined method `to_sym' for nil:NilClas

In which case it's enough to re-run brew update.

Now LEMON 1.3 can be installed via:

wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.tar.gz
tar xzvf lemon-1.3.tar.gz
cd lemon-1.3
cmake -DCMAKE_INSTALL_PREFIX=~/lemon -DCMAKE_CXX_COMPILER=/usr/local/bin/g++-4.8 -DCMAKE_C_COMPILER=/usr/local/bin/gcc-4.8
make install

Next step is to install boost:

brew install boost

Now compile xHeinz from the root of the git repository as follows. Note that CPLEX will be auto-detected if it's installed in ~/ILOG.

mkdir build
cd build
cmake -DCMAKE_CXX_COMPILER=/usr/local/bin/g++-4.8 -DCMAKE_C_COMPILER=/usr/local/bin/gcc-4.8 ..

On os 10.8.5, the auto-detection of the ILOG install directory failed, and the install dir must be specified explicitly, e.g. by running the following cmake command

cmake \
-DCMAKE_CXX_COMPILER=/usr/local/bin/g++-4.8 \
-DCMAKE_C_COMPILER=/usr/local/bin/gcc-4.8 \
-DCPLEX_INC_DIR=~/ILOG/cplex/include/ \
-DCPLEX_LIB_DIR=~/ILOG/cplex/lib/x86-64_osx/static_pic \
-DCONCERT_LIB_DIR=~/ILOG/concert/lib/x86-64_osx/static_pic \
-DCONCERT_INC_DIR=~/ILOG/concert/include/ ..

Next step is to compile the binary,

 make