SQMlauncher

R/Shiny interface to run and monitor SqueezeMeta pipelines (SqueezeMeta, SQM_reads, SQM_longreads) locally from your browser.

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Requirements

• SqueezeMeta installed via conda and available in your PATH
• The conda environment for SqueezeMeta must be active before installing or running the app

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Installation

We provide an installation script that handles all dependencies automatically. It uses mamba if available, falling back to conda otherwise.

1. Activate your SqueezeMeta conda environment:

conda activate SqueezeMeta   # or your environment name

2. Download and run the installation script:

bash install_sqmlauncher.sh

The script will:

• Install all required R/Shiny dependencies from conda-forge (precompiled binaries)
• Clone this repository into your conda environment
• Install the squeezeMetaR R package
• Add a convenience sqm() function to your ~/.Rprofile

Manual installation

If you prefer to install manually, first install the Shiny dependencies from conda-forge:

conda install -c conda-forge r-httpuv r-shiny r-shinyjs r-shinyfiles r-remotes

Then install the package from R:

remotes::install_local("/path/to/SQMlauncher/", 
                       force = TRUE, build = TRUE, 
                       build_vignettes = FALSE, upgrade = "never")

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Running the app

If you used the installation script, simply open R and run:

sqm()

Or manually:

library(squeezeMetaR)
lazyLoad(file.path(find.package("squeezeMetaR"), "R", "squeezeMetaR"), envir = globalenv())
run_app()

The interface will open in your default web browser.

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Features

• Execution profiles — pre-defined profiles for common use cases:
  • Standard Metagenome: default settings for Illumina/short-read data
  • Nanopore Metagenome: optimized settings for long-read data, with automatic adjustment of consensus and assembly parameters
• Real-time monitoring — live log updates and non-blocking pipeline execution via processx and shinyjs
• Path verification — checks for SqueezeMeta.pl on launch and warns if the environment is not correctly configured

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Troubleshooting

The app fails to start or the Run button does not respond:

• Make sure your SqueezeMeta conda environment is active
• Verify all dependencies are installed by re-running install_sqmlauncher.sh
• Check the R console for error messages
• Ensure you have write permissions in the Working Directory selected in the app

R cannot find run_app after library(squeezeMetaR):

This is a known issue in some conda environments where the package namespace does not load correctly. Use the lazyLoad workaround shown above, or reinstall using the provided script which configures this automatically via ~/.Rprofile.