Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.
GNU General Public License v3.0
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Add GitHub Actions workflow for building and testing #65
The provided GitHub Actions (GHA) workflow is designed for continuous integration and testing of the MetFamily R package. This workflow is triggered on push and pull requests events. It employs a matrix strategy, executing jobs on different operating systems (Linux, macOS, Windows) and R versions.
The workflow begins by defining environment variables and jobs, each specifying the operating system, R version, and associated configurations. It utilizes caching to speed up package installation and includes steps for checking dependencies, caching R packages, installing system dependencies based on the operating system, and handling BiocManager installations.
The workflow covers multiple aspects, including installing dependencies, running checks, testing coverage, and deploying the package. It employs conditionals to execute specific steps based on the operating system and package configurations.
The steps include setting up the R environment, checking out the repository, installing dependencies, caching packages, handling system dependencies, installing Bioconductor packages, running checks, revealing test details, and performing additional tasks like running RUnit tests, BiocCheck, and deploying the package.
Finally, the workflow uploads check results as artifacts in case of failure, aiding in diagnosing issues. This comprehensive GHA workflow ensures thorough testing and compatibility across different environments for the MetFamily R package.
The provided GitHub Actions (GHA) workflow is designed for continuous integration and testing of the MetFamily R package. This workflow is triggered on push and pull requests events. It employs a matrix strategy, executing jobs on different operating systems (Linux, macOS, Windows) and R versions.
The workflow begins by defining environment variables and jobs, each specifying the operating system, R version, and associated configurations. It utilizes caching to speed up package installation and includes steps for checking dependencies, caching R packages, installing system dependencies based on the operating system, and handling BiocManager installations.
The workflow covers multiple aspects, including installing dependencies, running checks, testing coverage, and deploying the package. It employs conditionals to execute specific steps based on the operating system and package configurations.
The steps include setting up the R environment, checking out the repository, installing dependencies, caching packages, handling system dependencies, installing Bioconductor packages, running checks, revealing test details, and performing additional tasks like running RUnit tests, BiocCheck, and deploying the package.
Finally, the workflow uploads check results as artifacts in case of failure, aiding in diagnosing issues. This comprehensive GHA workflow ensures thorough testing and compatibility across different environments for the MetFamily R package.