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python.sh
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python.sh
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#!/bin/bash
#-----------------------------
# Python
#-----------------------------
sudo apt-get install -y \
python3-pip
#-----------------------------
# pyenv
# https://github.com/yyuu/pyenv
#-----------------------------
mkdir -p ~/work/software/archives
cd ~/work/software/archives
git clone https://github.com/pyenv/pyenv.git ~/.pyenv
#from the pyenv readme
echo -e 'export PYENV_ROOT="$HOME/.pyenv"' \
'\nexport PATH="$PYENV_ROOT/bin:$PATH"' \
'\neval "$(pyenv init --path)"' \
'\neval "$(pyenv init -)"' >> ~/.bashrc
echo -e 'export PYENV_ROOT="$HOME/.pyenv"'\
'\nexport PATH="$PYENV_ROOT/bin:$PATH"'\
'\neval "$(pyenv init --path)"' | cat - ~/.profile > temp && mv temp ~/.profile
. ~/.profile
# In a non-interactive install, you can't do this:
# exec "$SHELL"
# and so you need to mock this:
export PYENV_ROOT="$HOME/.pyenv"
export PATH="$PYENV_ROOT/bin:$PATH"
eval "$(pyenv init -)"
pyenv install 3.8.10
pyenv shell 3.8.10
pip3 install --upgrade \
pip \
setuptools \
wheel
#-----------------------------
# pe2loaddata
#-----------------------------
cd ~
git clone https://github.com/broadinstitute/pe2loaddata.git
pip3 install --upgrade \
click \
PyYAML
cd pe2loaddata
pip3 install -e .
#-----------------------------
# DCP Control Node
# https://github.com/CellProfiler/Distributed-CellProfiler/wiki/Before-you-get-started%3A-setting-up
#-----------------------------
cd ~
git clone https://github.com/CellProfiler/Distributed-CellProfiler.git
pip3 install --upgrade \
awscli \
boto3
#-----------------------------
# cytominer-database
#-----------------------------
pip3 install cytominer-database