--------------------------------------------------- --- --- --- RNAMAP2D v. 1.7.5 --- --- --- --------------------------------------------------- A tool for calculation, analysis and visualization of contact maps for RNAs and protein-RNA structures. (c) 2009 - 2012 Michal J. Pietal, Natalia Szostak, Kristian Rother and Janusz M. Bujnicki See LICENSE.rtf for details on availability conditions. ------- INSTALLATION ON WINDOWS and MAC OS X ------- Please download the binary version, double click on an archive and extract it to any folder. Then, enter the folder and click the file RNAmap2D.exe/RNAmap2D.py.app to start the program. ---- INSTALLATION ON A FRESH UBUNTU 12.4 SYSTEM ---- Below the user might find the exact step-wise installation instructions of RNAmap2D program, on most popular and most recent stable (12.4 LTS) Ubuntu system. 1. Installing all available APT packages sudo apt-get install python2.7-dev sudo apt-get install python-wxgtk2.8 sudo apt-get install python-numpy sudo apt-get install python-egenix-mxtexttools sudo apt-get install python-excelerator sudo apt-get install python-cogent sudo apt-get install g++ 2. Installing the remaining packages from source a) Numeric - download Numeric-24.2.tar.gz file from http://sourceforge.net/projects/numpy/files/Old%20Numeric/24.2/ - change to the directory with the file - run following steps: tar -zvxf Numeric-24.2.tar.gz cd Numeric-24.2/ python setup.py build sudo python setup.py install b) Biopython - download biopython-1.42.tar.gz file from http://biopython.org/wiki/Download - change to the directory with the file - run following steps: tar -zvxf biopython-1.42.tar.gz cd biopython-1.42/ cp setup.py setup.py.old - edit the setup.py file, so that the diff command provides following output diff setup.py.old setup.py 387c387 < # 'Bio.KDTree', # disabled by default to avoid C++ compilation errors --- > 'Bio.KDTree', # disabled by default to avoid C++ compilation errors 444c444 < include_dirs=["Bio/Cluster"] --- > include_dirs=["Bio/Cluster","/usr/local/include/python2.7"] 446,451c446,452 < # CplusplusExtension('Bio.KDTree._CKDTree', # Disabled by default to avoid < # ["Bio/KDTree/KDTree.cpp", # C++ compilation errors < # "Bio/KDTree/KDTree.swig.cpp"], < # libraries=["stdc++"], < # language="c++" < # ), --- > CplusplusExtension('Bio.KDTree._CKDTree', # Disabled by default to avoid > ["Bio/KDTree/KDTree.cpp", # C++ compilation errors > "Bio/KDTree/KDTree.swig.cpp"], > libraries=["stdc++"], > language="c++", > include_dirs=["Bio/Cluster","/usr/local/include/python2.7"] > ), - run following steps: python setup.py build sudo python setup.py install 3. Downloading and running RNAmap2D - download rnamap2d_linux_py2.7.tar.gz file from ftp://ftp.genesilico.pl/pub/software/rnamap2d/ - change to the directory with the file - run following steps: tar -zvxf rnamap2d_linux_py2.7.tar.gz cd rnamap2d_py2.7 python RNAMAP2D.py -------- INSTALLATION ON OTHER UBUNTU LINUX -------- On Ubuntu Linux, the following packages need to be installed via apt-get or synaptic. The user can choose between python2.6 and python2.7 and use the proper RNAmap2D Linux distribution archive. python2.6 and its libraries: python2.6 (version 2.6.4) python2.6-dev (version 2.6.4) python-wxgtk2.8 (version 2.8.10) python-imaging (version 1.1.6) python-numeric (version 24.2) python-numpy (version 1.3) python-egenix-mxtexttools (version 3.1.2) python-excelerator (version 0.6.3) python-cogent (version 1.4) g++ (version 1.4.4) python2.7 and its libraries: python2.7 (version 2.7.3) python2.7-dev (version 2.7.3) python-wxgtk2.8 (version 2.8.12) python-imaging (version 1.1.7) python-numeric (version 24.2) python-numpy (version 1.6.1) python-egenix-mxtexttools (version 3.2.1) python-excelerator (version 0.6.4) python-cogent (version 1.5.1) g++ (version 4.6.3) In addition, BioPython version 1.42 needs to be installed from source (see http://biopython.org/wiki/Download ). IMPORTANT: uncomment all lines mentioning 'KDTree' in setup.py before running 'python setup.py build'. If you have a newer BioPython version installed already, you can copy Bio/ and Martel/ from the build/lib.linux.. directory to the RNAMap2D directory. Please note, that other program versions, especially of wxPython and BioPython will not work. ----------- INSTALLATION ON ANY OTHER LINUX ----------- The installation of the Linux distribution requires some third-party programs. Please make sure all the following libraries are installed: Python 2.6 = 2.6.4 (available at http://www.python.org ) Python Imaging Library (PIL) = 1.1.6 (available at http://www.pythonware.com/products/pil/ ) Numeric = 24.2 (available at http://sourceforge.net/projects/numpy/files/Old Numeric/) (after installing, the Lib folder should be copied into python's dist-packages/ dir as Numeric ) Numpy = 1.3 (available at http://numpy.scipy.org/ ) mxTextTools = 3.1.2 (available at http://www.egenix.com/products/python/mxBase/) wxPython = 2.8.10 (available at http://sourceforge.net/projects/wxpython/files/wxPython/ ) PyExcelerator = 0.6.3 (available at http://sourceforge.net/projects/pyexcelerator/ ) BioPython = 1.42 (available at http://biopython.org/wiki/Download ) IMPORTANT: uncomment all lines mentioning 'KDTree' in setup.py before running 'python setup.py build'. If you have a newer BioPython version installed already, you can copy Bio/ and Martel/ from the build/lib.linux.. directory to the RNAMap2D directory. PyCogent = 1.4 is (available at http://sourceforge.net/projects/pycogent/) g++ and python2.6-dev packages are either present or easy to download in any other Linux systems. Please refer to the respective manuals. Alternatively, the user can create or enhance python2.7 environment using library versions listed in the previous paragraph. We support the listed modules only. Whilst RNAmap2D should work on above, we give no warranty on it since it was not tested on other library combinations. That's why we strongly recommend to use the strict library versions (as listed), all the more they're all available to the date of program's release. ----------- INSTALLATION OF RNAVIEW ON LINUX or MACOSX (OPTIONAL) ----------- RNAMAP2D can use the RNAView program to calculate base pairs. If it is not found, RNAMAP2D will use its own module for that. To make RNAView available to RNAMAP2d, please install rnaview (available at http://ndbserver.rutgers.edu/services/download/ ) after the installation create a link to the RNAView binary in /usr/bin by typing: sudo ln -s /?/?/?/RNAVIEW/bin/rnaview /usr/bin and add to your ~/.bashrc file the line: export RNAVIEW=/usr Note that $RNAVIEW variable has to be set to /usr as well. ----------- USAGE ----------- Linux: Unpack the archive (using tar -zvxf command) Change directory to rnamap2d and type: python RNAMAP2D.py (if multiple Python instalations are present, type python2.6 instead of python). This will start a self-explanatory GUI. MacOSX: Unpack the archive by double clicking it. Then enter rnamap2d directory and double click the RNAMAP2D.py.app file For more information about usage please see the RNAmap2D manual and tutorial available from the homepage: http://iimcb.genesilico.pl/rnamap2d.html Windows: Unpack the archive by double clicking it. Then enter rnamap2d directory and double click the RNAMAP2D.exe file For more information about usage please see the RNAmap2D manual and tutorial available from the homepage: http://iimcb.genesilico.pl/rnamap2d.html ----------- TROUBLESHOOTING ----------- - The library msvcp90.dll under Windows may be missing. Plese download it from: http://www.dll-files.com/dllindex/dll-files.shtml?msvcp90 - An already installed wxPython 2.6 may interfere with your wxPython 2.8 package. Use python2.6 command instead of python to run the program.