Hi,
OK, this issue is solved. Now, everything (anaconda, rdkit, ipython notebook
jupiter) runs fine.
I documented the installation process. In case anyone is interested here is my
installation script. I did not run it a last time, but it should be at least a
good start to install and run rdkit in a python notebook within an anaconda
environment.
regards
Soren
------------ rdkit_anaconda_install.sh -----------------------
#!/bin/bash
sourcedir=/tmp/install_modeling_env
mkdir /tmp/install_modeling_env
cd /tmp/install_modeling_env
install_prefix=/path/to/target/dir
#Check target exists
if [ -d $install_prefix ] ;then
echo "Please create target directory first"
exit 1
fi
export PATH=$PATH:$install_prefix/bin
yum -y install wget tar bzip2 git gcc-c++ patch python-qt4 @development-tools
boost\
boost-devel cmake bison python-devel tk-devel readline-devel\
zlib-devel bzip2-devel sqlite-devel
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
chmod +x Miniconda-latest-Linux-x86_64.sh
$sourcedir/Miniconda-latest-Linux-x86_64.sh -b -p $install_prefix
git clone https://github.com/rdkit/conda-rdkit.git conda-rdkit
conda update conda
conda update --all
conda install --yes pip
conda install --yes numpy
conda install --yes scipy
conda install --yes matplotlib
conda install --yes ipython
conda install --yes pil
conda install --yes scikit-learn
conda install --yes scikit-image
conda install --yes pandas
conda install --yes requests
conda install --yes conda-build
conda install --yes patchelf
conda install --yes jinja2
conda install --yes pyzmq
conda install --yes tornado
conda install --yes jsonschema
conda install --yes xwpython
conda update --all
cd $sourcedir/conda-rdkit && conda build boost
cd $sourcedir/conda-rdkit && conda build rdkit
cd $sourcedir
conda create --use-local -n env rdkit ipython matplotlib requests pyzmq pyqt
jinja2 tornado jsonschema pil scikit-learn pandas wxpython
rm -r $sourcedir
source activate env
echo "NOTE Remember to add 'export PATH=\$PATH:$install_prefix/bin' to you PATH"
echo "NOTE Start the notebook with 'source activate env ; ipython notebook ;
source deactivate '
------------------------------------------------------------------------------
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