rNAV2.0 COMPILATION INSTRUCTIONS ================================ Dependencies List - Ubuntu ========================== 1.Dependencies that are NOT distributed with rNAV -cmake 2.8.7 -libfreetype6-dev 2.4.8 -libqt4-dev 4.8.1 -libjpeg-dev 8c -libpng12-dev 1.2.46 -libglew-dev 1.5 -libxml2-dev 2.7.8 -NumPy 1.6.1 -biopython 1.63 -setuptools 2.2 -qt4-dev-tools 4.8.1 -sphinx 1.1.3 2.Dependencies that are distributed with rNAV and automatically compiled and installed (you can find them under .../rNAV2.0/thirdparty directory) -Fasta 36 -suds 0.4 -tulip 3.8 3. Optional -intarna-1.2.5 -ViennaRNA-1.8.5 -cmake-gui (On various plateform, this is directly provided by the cmake package) Quick Installation (for the impatient) ================== Install all dependencies with a single command line: > sudo apt-get install cmake libfreetype6-dev libqt4-dev libjpeg-dev libpng12-dev libglew-dev libxml2-dev python-numpy python-scipy python-biopython python-setuptools qt4-dev-tools python-sphinx [or install one by one: > sudo apt-get install cmake > sudo apt-get install libfreetype6-dev > sudo apt-get install libqt4-dev > sudo apt-get install libjpeg-dev > sudo apt-get install libpng12-dev > sudo apt-get install libglew-dev > sudo apt-get install libxml2-dev > sudo apt-get install python-numpy python-scipy > sudo apt-get install python-biopython > sudo apt-get install python-setuptools > sudo apt-get install qt4-dev-tools > sudo apt-get install python-sphinx ] > tar -xvzf rNAV2.0.tar.gz [If you want to use IntaRNA from the University of Freiburg, install it now by typing: > ../getThirdparty.sh] > cd rNAV2.0/build > cmake .. > make > make install > ../rNAV Basic Installation ================== These are generic installation instructions. CMake is the main build system. You need to be root for many dependencies but not for rNAV itself. The easiest way to compile this package is: 1. untar rNAV2.0.tar.gz 2. If you want to use IntaRNA interaction prediction tool, you will have to download and install it. You can do this automatically by typing: > ../getThirdparty.sh or manually: - download it from the University of Freiburg site (http://www.bioinf.uni-freiburg.de/Software/). - download its dependencie : Vienna RNA Package (http://www.tbi.univie.ac.at/~ivo/RNA/) - unpack both package and put the resulting folders under .../rNAV2.0/thirdparty/. rNAV CMakeLists will handle compilation and installation for you. 3.'cd' to rNAV build directory (i.e. .../rNAV2.0/build/), and type `cmake ..`. This will check for all of rNAV and tulip dependencies, and warn if some are missing. If you want to build with debug informations, or with optimisations, you need to tell CMake to do so. You can either use `cmake -i`, which will ask you what kind of build you want (Debug/Release), or invoke cmake like this: `cmake .. -DCMAKE_BUILD_TYPE=Release` (or Debug). 4. Install all dependencies that you don't have - install cmake > sudo apt-get install cmake - install libfreetype6-dev > sudo apt-get install libfreetype6-dev - install Qt4 > sudo apt-get install libqt4-dev - install libjpeg > sudo apt-get install libjpeg-dev - install libpng12-dev > sudo apt-get install libpng12-dev - install libglew-dev > sudo apt-get install libglew-dev - install libxml2-dev > sudo apt-get install libxml2-dev - install NumPy > sudo apt-get install python-numpy python-scipy - install biopython > sudo apt-get install python-biopython - install setuptools > sudo apt-get install python-setuptools - install qt-assistant > sudo apt-get install qt4-dev-tools - install sphinx > sudo apt-get install python-sphinx 5. Type `cmake ..` 6. Type `make` to compile the packages. 7. Type `make install` to install the programs and any data files and documentation. Compilers and Options --------------------- You can pass options to cmake, either by using `cmake .. -i` or `cmake-gui ..`, which will provide you with some control over the build. You can change the build type (Debug Vs. Release) and compilation options. If Cmake cannot find some external libraries you can set yourself the location of these libraries. Installation Names ================== By default, `make install' will install the package's files in `.../rNAV2.0/install/'. You can specify another installation prefix by giving cmake' the option `-DCMAKE_INSTALL_PREFIX=PATH'. Be careful not to use "-" character in file paths (because of "ssearch" that do not support). Running rNAV ============ To run rNAV launch the 'rNAV' script located in the .../rNAV2.0/ directory or the one located in the /bin directory of the installation directory. 'installation_directory/bin/rNAV'