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agladstein edited this page Jan 23, 2018 · 1 revision

Install

cd to the directory you want to work in,

git clone https://github.com/agladstein/SimPrily.git

Environment Set up

Python 2.7.6, 2.7.11, or 2.7.13 is required to run the code, with the requirements installed from requirements.txt. We highly recommend running SimPrily with the Docker image or virtual environment.

Docker

A Docker Image built with Python 2.7.13, the requirements, and the SimPrily code can be found on Docker Hub https://hub.docker.com/r/agladstein/simprily_autobuild/

The Docker image can be pulled with

docker pull agladstein/simprily_autobuild

Singularity

A Singularity Image, built from the Docker Image, is used for the Open Science Grid workflow. The Singularity Image is NOT currently publically available through Singularity Hub.

Virtual environment

The most reliable way to do this is with a virtual environment.

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install python-virtualenv git python-dev
sudo easy_install -U distribute
virtualenv simprily_env
source simprily_env/bin/activate
cd SimPrily
pip install --upgrade pip
pip install pip-tools
pip-sync
simprily_env/bin/python simprily.py --help

If you get an error during pip-sync try rebooting the system.

Virtual Machine for non-Linux

If you are running on a non-Linux OS, we recommend using the virtual machine, Vagrant (can be used on Mac or PC). In order to run Vagrant, you will also need VirtualBox.
Download Vagrant from https://www.vagrantup.com/downloads.html
Download VirtualBox from https://www.virtualbox.org/

vagrant up
vagrant ssh
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install python-virtualenv git python-dev
sudo easy_install -U distribute
cd ~
virtualenv simprily_env
source ~/simprily_env/bin/activate
pip install --upgrade pip
pip install pip-tools
cd /vagrant
pip-sync
~/simprily_env/bin/python simprily.py --help

Local installation

If the above options do not work, the correct version of Python can also be installed locally:

cd mkdir python_prebuild
wget https://www.python.org/ftp/python/2.7.6/Python-2.7.6.tgz
mkdir python
tar -zxvf Python-2.7.6.tgz
cd Python-2.7.6
./configure --prefix=$(pwd)/../python
make
make install
cd ..
export PATH=$(pwd)/python/bin:$PATH
wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py
pip install -r /home/agladstein/simslg/macsswig_simslg/requirements.txt
python simprily.py --help
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