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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.

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
cluster/180.1563455908.txt.gz · Last modified: 2019/07/18 09:18 by hmeij07