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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.
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]
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Remarkably complex compilations.