Global pairwise network alignment
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README.md

natalie

Global pairwise network alignment

Dependencies

  • LEMON 1.3
  • Optional: ILOG CPLEX (>= 12.0)

Compiling

Get natalie from github:

git clone <HTTPS clone URL (see on the right side of this page)>

First, LEMON 1.3 needs to be installed:

wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.tar.gz
tar xvzf lemon-1.3.tar.gz
cd lemon-1.3
cmake -DCMAKE_INSTALL_PREFIX=~/lemon
make install

Note: On Mac OS 10.9, comment out the following two lines and add the code below at line 162 in CMakeLists.txt before make install

#ADD_SUBDIRECTORY(demo) 
#ADD_SUBDIRECTORY(tools)

if( ${CMAKE_SYSTEM_NAME} MATCHES "Darwin" )
  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++ " )
endif()

You can remove the LEMON sources now, i.e., rm -rf lemon-1.3. Next, natalie can be compiled:

mkdir build
cd build
cmake ..
make

In case auto-detection of LEMON or CPLEX fails, do

cmake \
-DLIBLEMON_ROOT=~/lemon \
-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/ ..

Running natalie

To run natalie:

./natalie -if1 0 -if2 0 -ifm 0 -g1 ../data/rno.gml -g2 ../data/hsa.gml -gm ../data/rno_hsa.seqSim
./natalie-cpx -if1 0 -if2 0 -ifm 0 -g1 ../data/rno.gml -g2 ../data/hsa.gml -gm ../data/rno_hsa.seqSim

For usage instructions specify -h.