Installation

Prerequisites

• Julia version 1.9.3 or higher
• Git (for development installation)

Basic Installation

To install StochasticGene.jl, open the Julia REPL and run:

using Pkg
Pkg.add("StochasticGene")

Development Installation

To install the development version:

using Pkg
Pkg.develop(url="https://github.com/nih-niddk-mbs/StochasticGene.jl")

Required Packages

The following packages will be automatically installed as dependencies:

• Distributions
• StatsBase
• DataFrames
• CSV
• Plots
• ProgressMeter
• MCMCChains
• Turing
• DifferentialEquations
• Optim
• ForwardDiff
• SpecialFunctions
• Random
• Statistics
• LinearAlgebra

Verification

To verify the installation, run:

using StochasticGene

If no errors occur, the package is installed correctly.

Troubleshooting

If you encounter any issues during installation:

1. Ensure you have the correct Julia version (1.9.3 or higher)
2. Try updating your package registry:

   using Pkg
   Pkg.update()

3. If problems persist, check the GitHub Issues page for known issues
4. For additional help, open a new issue on GitHub

Local Installation

To install StochasticGene on your computer:

julia> ] add StochasticGene

To test the installation:

julia> ] test StochasticGene

To update to the latest version:

julia> ] update StochasticGene

Biowulf Installation (NIH HPC)

1. Start an interactive session:

[username@biowulf ~]$ sinteractive --constraint=x2695 --mem=64G

1. Load Julia:

[username@biowulf ~]$ module load julialang
[username@biowulf ~]$ julia -t 1

1. Install StochasticGene:

julia> ] add StochasticGene

1. Next: for swarm files, makeswarm, merging single-unit rates for coupled fits, and the recommended individual-units-then-merge workflow, read Cluster and batch workflows in this manual (also linked from the documentation home page).

If you encounter Julia crashes after an update, remove your Julia depot and reinstall:

[username@biowulf ~]$ rm -r --force .julia

Then start Julia and re-add StochasticGene as above.

Requirements

• Julia 1.9.3 or higher
• Required packages will be automatically installed during installation