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OpenStructure

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.”

OpenStructure relies on these applications and Python 2.7.15. All applications including Python need to compiled with –enable-share in the configuration step. A step by step process is listed below. 

-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   python
--   unit_test_framework
--   filesystem
--   system
--   iostreams
--   program_options
--   regex
--   thread
-- Found ZLIB: /share/apps/CENTOS6/zlib/1.2.11/lib/libz.so (found version "1.2.11")
-- Found PNG: /share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so (found version "1.2.49")
-- Found EIGEN: /share/apps/CENTOS6/eigen/3.2.10
-- Numpy headers found
-- 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")


====== Compilations ======

Use ''gcc'' => 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`
./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

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-shared --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



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
# 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

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

# setup the environment egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt

ost –help Usage: 

  ost [ost options] [script to execute] [script parameters]

or 

  ost [action name] [action options]

</code>

Remarkably complex compilations.

cluster/180.1563451335.txt.gz · Last modified: by hmeij07