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
2. Try updating your packages: Pkg.update()
3. Check the GitHub issues for known problems
4. Open a new issue if your problem persists

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

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