Install and 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. Environments for Python 3 will soon be available.
We highly recommend running SimPrily with the provided Docker, Singularity, or virtual environment.

Container¶

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/

cd to the directory you want to work in and then pull the Docker image. To pull the Docker container:

docker pull agladstein/simprily

Singularity¶

The Docker image can be pulled as a Singularity container.

To pull the Singularity container:

singularity pull docker://agladstein/simprily

Open Science Grid Connect¶

A prebuilt Singularity Image from the Docker Image is used for the Open Science Grid workflow. The Singularity Image on OSG Connect is available from /cvmfs/singularity.opensciencegrid.org/agladstein/simprily\:latest.

Virtual environment¶

Linux OS¶

cd to the directory you want to work in and then download the repository,

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

Install the virtual environment and install the requirements.

./setup/setup_env_2.7.sh

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/

cd to the directory you want to work in and then download the repository,

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

Start Vagrant, ssh into Vagrant, cd to SimPrily directory.

vagrant up
vagrant ssh
cd /vagrant

Install the virtual environment and install the requirements.

./setup/setup_env_vbox_2.7.sh

Local installation¶

We do not recommend this method

cd to the directory you want to work in and then download the repository,

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

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 requirements.txt
python simprily.py --help