This repository contains the Snakemake workflows for the SBpipe project. The workflows are:

• parameter estimation (pe)
• simulation (sim)
• single parameter scan (ps1)
• double parameter scan (ps2)

To run these workflows SBpipe and Snakemake must be installed.

• non-Miniconda users: see the documentation to install these packages
• Miniconda users: see below

Therefore:

# clone workflow into working directory
git clone https://github.com/pdp10/sbpipe_snake.git project_name
cd project_name

######################
# Miniconda users ONLY
# install dependencies into isolated environment
conda env create -n sbpipe_snake --file environment.yaml

# activate environment
conda activate sbpipe_snake
######################

# create a folder Models and populate it with
# the mathematical models (see `SBpipe`_) to run.
mkdir Models

# edit config_[sim|ps1|ps2|pe].yaml as needed for your models
# e.g. for model simulation
vim config_sim.yaml

# execute workflow, deploy software dependencies via conda
# e.g. parameter estimation workflow
snakemake -s sbpipe_sim.snake --configfile config_sim.yaml