Created by
Dénes Türei
| #!/usr/bin/bash
# Denes Turei EMBL 2018
# turei.denes@gmail.com
# install pip from python3.6
curl https://bootstrap.pypa.io/get-pip.py | python3.6
# downgrading pip because version 10 has
# unresolved issues
python3.6 -m pip install --upgrade pip==9.0.3
# fixing the issue we already fixed
sed -i 's/orig_path.sort(key=position_in_sys_path)/orig_path = sorted(orig_path, key = position_in_sys_path)/' /usr/local/lib/python3.6/dist-packages/pip/_vendor/pkg_resources/__init__.py
# installing python 3.6 C headers
# in order to be able to compile igraph
apt install python3.6-dev libigraph0-dev
# install igraph python bindings
mkdir -p build/python-igraph
cd build/python-igraph
curl -LO https://github.com/igraph/python-igraph/archive/master.zip
unzip master.zip
cd python-igraph-master
python3.6 ./setup.py develop --c-core-url https://github.com/igraph/igraph/archive/master.tar.gz
python3.6 ./setup.py install
cd ../../..
rm -r build
# remove python 3 numpy installation
# and install numpy properly for python 3.6
# same for scipy, lxml, pandas, statsmodels,
# pygraphviz and pycurl
# these are all packages with C bindings
# no wonder they can't be loaded if compiled
# against different version
pip3 uninstall -y numpy scipy pandas lxml statsmodels pycurl pygraphviz bs4 html5lib
pip3.6 install numpy scipy pandas lxml statsmodels pycurl pycairo pygrphviz bs4 html5lib
pip3.6 install --upgrade bs4
# install pypath for python3.6
pip3.6 install pypath-0.7.73.tar.gz
# install jupyter and ipython kernel for python3.6
# btw very weird, jupyter loaded anaconda python 2.7
# kernel when python 3 kernel was requested...
pip3.6 install jupyter
# registering python 3.6 shell as an ipython kernel
python3.6 -m ipykernel install
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