Saturation mutagenesis MPRA data access portal

Shiny webapp of https://mpra.gs.washington.edu/satMutMPRA or https://kircherlab.bihealth.org/satMutMPRA/.

Installation

Option 1: conda

If not already done install miniconda

set up the channels:

conda config --add channels bioconda
conda config --add channels conda-forge

Then run conda install mpra-data-access-portal

The latest version on conda is 0.1.11 so you can run conda install mpra-data-access-portal=0.1.11 to install exactly this version.

now you can run the data portal via the command: mpra-data-access-portal

The default port is 8080 and the default host 0.0.0.0. If you want to change this please change the two variables SHINY_PORT and export SHINY_HOST. E.g.:

export SHINY_PORT=7001
export SHINY_HOST=127.0.0.1

Then run mpra-data-access-portal again.

Option 2: from source

install dependencies:

R version 4.3.3

R packages:

• dplyr version 1.1.4
• DT version 0.33
• ggplot2 version 3.5.1
• shiny version 1.9.1
• shinytest2 version 0.3.1
• shinyvalidate 0.1.3
• htmlwidgets version 1.6.4
• readr version 2.1.5
• stringr version 1.5.1
• plotly version 4.10.4

You can install also via conda using: conda env create -f environment.yaml -n mpra-data-access-portal

Get the latest version via version release on github: https://github.com/kircherlab/MPRA_SaturationMutagenesis/archive/v0.1.11.tar.gz or cloning the repository: https://github.com/kircherlab/MPRA_SaturationMutagenesis/archive/v0.1.11.tar.gz and change to the version tag v0.1.11.

the goto the directory and run the shiny server (here on port 8080 and on host 0.0.0.0, if not alredy defined:

export SHINY_HOST=${SHINY_HOST-0.0.0.0}
export SHINY_PORT=${SHINY_PORT-8080}

Rscript -e "shiny::runApp(port = ${SHINY_PORT}, launch.browser = FALSE, host = '${SHINY_HOST}')"

Development

Setting up the development environment

To set up a development environment, use conda with the provided environment.yml:

conda env create -f environment.yml -n satMutMPRA
conda activate satMutMPRA

Running tests

To run the test suite:

conda activate satMutMPRA
Rscript run_tests.R

Tests verify:

• All required packages are available
• Data files exist and have expected format
• Application code has valid syntax
• Markdown documentation files are present

Releases

This project uses Release Please to automate versioning and release management.

How releases work

Releases are automatically created when commits are pushed to master using Conventional Commits. The Release Please action will:

1. Analyze commit messages on master
2. Create a release PR with updated DESCRIPTION version and CHANGELOG
3. Once merged, automatically create a GitHub release with:
   • Release notes generated from commit history
   • Packaged artifacts (tar.gz and zip files)
   • Tests run to verify the release

Making a release

Simply use conventional commit messages in your pull requests:

• feat: - New features (triggers minor version bump: 0.1.11 → 0.2.0)
• fix: - Bug fixes (triggers patch version bump: 0.1.11 → 0.1.12)
• BREAKING CHANGE: - Major changes (triggers major version bump: 0.1.11 → 1.0.0)

Example:

git commit -m "feat: add support for new reference genome"
git commit -m "fix: update filter logic for edge cases"

When you merge a PR with such commits, Release Please will automatically:

• Create a release PR updating the version
• Update CHANGELOG.md
• Merge and create the GitHub release

Releases are available at: https://github.com/kircherlab/MPRA_SaturationMutagenesis/releases