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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.” Please visit their web site for more details.

v 1.9 installed
https://openstructure.org/
recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt

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.

-- 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")



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

# invoke CLI
ost --help
Usage:

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

or
    ost [action name] [action options]

Compilations

Use gcc greater than or equal to 4.5

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

Remarkably complex compilations.

Notes (from developers):

With the 1.10 release, you won't need the “brute fix for boost to find libs anymore. This page instructions to be for 1.9 by either doing a “git checkout 1.9.0” after “cd openstructure-1.9” or by fetching a tagged tar ball directly (in gitlab, the URL for that would be
https://git.scicore.unibas.ch/schwede/openstructure/repository/1.9.0/archive.tar.gz
where “1.9.0” can be replaced with any git-tag).

cmake.log

-- The CXX compiler identification is GNU 4.8.4
-- The C compiler identification is GNU 4.8.4
-- Check for working CXX compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/c++
-- Check for working CXX compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/gcc
-- Check for working C compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of void*
-- Check size of void* - done
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   python
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   unit_test_framework
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   filesystem
--   system
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   iostreams
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   program_options
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   regex
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   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") 
-- LSB-Release system information::
           LSB Distributor-ID: centos
           LSB Release: 6.10
           LSB Codename: final
           System bit type: 64 bit
-- OpenStructure will be built with the following options:
   Install Prefix                        (-DPREFIX) : /share/apps/CENTOS6/openstructure/1.9
   RPath in install                   (-DUSE_RPATH) : OFF
   Info support                     (-DENABLE_INFO) : OFF
   Graphical interface               (-DENABLE_GUI) : OFF
   OpenGL support                    (-DENABLE_GFX) : OFF
   OpenGL via Mesa                     (-DUSE_MESA) : 
   Image Processing support          (-DENABLE_IMG) : ON
   Shader support                    (-DUSE_SHADER) : OFF
   Numpy support                      (-DUSE_NUMPY) : ON
   SpaceNav Device support         (-DENABLE_SPNAV) : OFF
   OpenMM support                     (-DENABLE_MM) : OFF
   OpenMM plugins            (-DOPEN_MM_PLUGIN_DIR) : NONE
   Optimize                            (-DOPTIMIZE) : OFF
   Profiling support                    (-DPROFILE) : OFF
   Double Precision        (-DUSE_DOUBLE_PRECISION) : OFF
   Compound Lib                    (-DCOMPOUND_LIB) : NONE
   TMAlign and TMScore          (-DCOMPILE_TMTOOLS) : OFF
   Static Libraries               (-DENABLE_STATIC) : OFF
   Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : OFF
   Hidden object visibility  (-DHIDDEN_VISIBILITY) : OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/src/tmp/openstructure-1.9

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Table of Contents

OpenStructure

Compilations

cmake.log