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cluster:180 [2019/07/18 11:54]
hmeij07 created 		cluster:180 [2019/07/18 12:16]
hmeij07
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 +\\
 +**[[cluster:0|Back]]**
 +
 +
 +
 ====== OpenStructure ====== ====== OpenStructure ======
  
-Open-Source Computational Structural Biology Framework+Open-Source Computational Structural Biology Framework. "This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics." Please visit their web site for more details.
  
-  * v 1.9+  * v 1.9 installed
   * https://openstructure.org/   * https://openstructure.org/
   * recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt   * recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt
  
-OpenStructure relies on these applications and Python 2.7.15 (see python2 section).+OpenStructure relies on these applications and Python 2.7.15. All applications including Python need to compiled with --enable-share in the configuration step, if possible.  A step by step process is listed below.
  
 <code> <code>
Line 27: Line 32:
 -- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so -- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so
 -- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9") -- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9")
 +
 +</code>
 +
 +====== Compilations ======
 +
 +Use ''gcc'' greater than or equal to 4.5
 +
 +<code>
 +
 +export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH
 +
 +export PATH=/share/apps/CENTOS6/cmake/3.12.1/bin:$PATH
 +
 +tar zxvf ../Python-2.7.15.tgz                                                                                                       
 +cd Python-2.7.15/ 
 +./configure --prefix=/share/apps/CENTOS6/python/2.7.15 --enable-shared                                                              
 +export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH
 +python ../get-pip.py                                                                                                                
 +pip install numpy scipy 
 +
 +wget https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz
 +tar zxvf boost_1_68_0.tar
 +cd boost_1_68_0.tar
 +./bootstrap.sh --prefix=/share/apps/CENTOS6/boost/1.68.0 \
 +--with-python=/share/apps/CENTOS6/python/2.7.15/bin/python \
 +--with-python-root=/share/apps/CENTOS6/python/2.7.15
 +./b2 install
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/boost/1.68.0/lib:$LD_LIBRARY_PATH
 +
 +# brute fix for boost to find libs
 +cp -p libboost_python27.a libboost_python.a
 +cp -p libboost_python27.so.1.68.0 libboost_python.so
 +
 +wget http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz
 +mv ../3.2.10.tar.gz ../eigen-3.2.10.tar.gz
 +tar zxvf ../eigen-3.2.10.tar.gz
 +cd eigen-eigen-b9cd8366d4e8/
 +mkdir build
 +cd build
 +cmake ..  -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS6/eigen/3.2.10
 +make blas
 +make install
 +scp -rp ./* /share/apps/CENTOS6/eigen/3.2.10/
 +
 +wget http://fftw.org/fftw-3.3.8.tar.gz
 +tar zxvf ../fftw-3.3.8.tar.gz
 +cd fftw-3.3.8/
 +mkdir -p /share/apps/CENTOS6/fftw/3.3.8-enable-single
 +./configure --enable-share --enable-single \
 +--prefix=/share/apps/CENTOS6/fftw/3.3.8-enable-single
 +make
 +make install
 +export PATH=/share/apps/CENTOS6/fftw/3.3.8-enable-single/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/fftw/3.3.8-enable-single/lib:$LD_LIBRARY_PATH
 +
 +tar zxvf ../zlib-1.2.11.tar.gz
 +cd zlib-1.2.11/
 +./configure --prefix=/share/apps/CENTOS6/zlib/1.2.11
 +make
 +make install
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/zlib/1.2.11/lib:$LD_LIBRARY_PATH
 +
 +tar zxvf ../libpng-1.6.37.tar.gz
 +cd libpng-1.6.37/
 +./configure --prefix=/share/apps/CENTOS6/lpng/1.6.37
 +make
 +make install
 +export PATH=/share/apps/CENTOS6/lpng/1.6.37/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/lpng/1.6.37/lib:$LD_LIBRARY_PATH
 +
 +tar xvfz ../tiff-4.0.9.tar.gz
 +cd tiff-4.0.9/
 +./configure --prefix=/share/apps/CENTOS6/tiff/4.0.9
 +make
 +make install
 +export PATH=/share/apps/CENTOS6/tiff/4.0.9/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/tiff/4.0.9/lib:$LD_LIBRARY_PATH
 +
 +# openstructure
 +
 +git clone https://git.scicore.unibas.ch/schwede/openstructure.git openstructure-1.9
 +cd openstructure-1.9/
 +cd /share/apps/CENTOS6/boost/1.68.0/lib
 +
 +rm -f cmakelog; cmake \
 +-DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS6/openstructure/1.9 \
 +          -DBOOST_ROOT=/share/apps/CENTOS6/boost/1.68.0 \
 +         -DPYTHON_ROOT=/share/apps/CENTOS6/python/2.7.15 \
 +  -DEIGEN3_INCLUDE_DIR=/share/apps/CENTOS6/eigen/3.2.10 \
 +        -DFFTW_LIBRARY=/share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so \
 +    -DFFTW_INCLUDE_DIR=/share/apps/CENTOS6/fftw/3.3.8-enable-single/include \
 +        -DZLIB_LIBRARY=/share/apps/CENTOS6/zlib/1.2.11/lib/libz.so \
 +    -DZLIB_INCLUDE_DIR=/share/apps/CENTOS6/zlib/1.2.11/include \
 +         -DPNG_LIBRARY=/share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so \
 +     -DPNG_INCLUDE_DIR=/share/apps/CENTOS6/lpng/1.6.37/include \
 +        -DTIFF_LIBRARY=/share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so \
 +    -DTIFF_INCLUDE_DIR=/share/apps/CENTOS6/tiff/4.0.9/include \
 +-DENABLE_GUI=OFF -DENABLE_GFX=OFF -DENABLE_INFO=OFF \
 +-DUSE_NUMPY=ON -DENABLE_MM=OFF \
 +-DENABLE_STATIC=OFF | tee cmake.log
 +make
 +make install
 +
 +# [100%] Built target actions
 +
 +export PATH=/share/apps/CENTOS6/openstructure/1.9/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/openstructure/1.9/lib64:$LD_LIBRARY_PATH
 +
 +</code>
 +
  
  
 # setup the environment # setup the environment
-`egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt`+egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt
  
 ost --help ost --help
cluster/180.txt ยท Last modified: 2019/07/31 18:56 by hmeij07

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