lana

Local pairwise network alignment

Authors

• Jelmer Mulder
• Mohammed El-Kebir
• Gunnar W. Klau

Dependencies

• LEMON 1.3
• Boost

Compiling

Get lana 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, lana can be compiled:

mkdir build
cd build
cmake ..
make

• Boost

Compiling

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

cmake -DLIBLEMON_ROOT=~/lemon ..

If desired, the flags -DCMAKE_C_COMPILER and -DCMAKE_CXX_COMPILER can be used with the cmake command to specify a different compiler.

Running lana

For complete run instructions, please run

 ./lana -h

An example invocation (all exact matches of min size 6 between mouse and worm):

./lana -if1 0 -if2 0 -ifm 0 -g1 ../data/mmu.gml -g2 ../data/cel.gml -gm ../data/mmu_cel.seqSim -mcs 6 -o lana_mmu_cel.out