What HPC environments are supported?

It is optimized for Linux-based HPC and cloud systems, providing specific integration patterns for SLURM, Bioconda, and Rclone.

How are external tool integrations tested?

Integrations are tested using a specific environment flag (MYCELIA_RUN_EXTERNAL=true) and rely on simulated inputs and default database paths to ensure stability.

What is the primary goal of the Mycelia project?

Mycelia is a platform for multiomic analysis and biological characterization, designed to facilitate data integration, prediction, and design in biological systems.

Does this skill help with software reproducibility?

Yes, it enforces version pinning, input/output specification tracking, and provenance information for every external tool integrated into the system.

How does this skill handle citations for bioinformatics tools?

The skill mandates that all third-party tools, databases, and algorithms include specific DOI or paper references in code comments, README files, and manuscript methods sections.

Bioinformatics Tool Integration

Name: Bioinformatics Tool Integration
Author: cjprybol

bycjprybol

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Data Science & ML

Standardizes the integration, citation, and testing of external bioinformatics tools within the Mycelia multiomic framework.

About

This skill provides Claude with specific protocols for wrapping third-party bioinformatics software within the Mycelia repository, ensuring that external tool calls are isolated and maintainable. It enforces best practices for high-performance computing (HPC) compatibility with SLURM and Bioconda, while mandating strict citation requirements for databases and algorithms to ensure research reproducibility. By following these patterns, developers can easily extend Mycelia's multiomic capabilities while keeping codebases organized and ready for scientific publication.

Key Features

6 GitHub stars
HPC-ready integration with SLURM, Bioconda, and Rclone
Automated citation enforcement for tools, databases, and DOIs
Isolated helper architecture for third-party tool wrappers
Standardized testing protocols using the MYCELIA_RUN_EXTERNAL flag
Reproducibility tracking through version pinning and provenance data

Use Cases

Ensuring all external software and data sources are properly cited for a manuscript
Configuring bioinformatics workflows to run reliably on Linux-based HPC clusters
Integrating new sequence alignment or assembly tools into a multiomic pipeline

About

Key Features

6 GitHub stars
HPC-ready integration with SLURM, Bioconda, and Rclone
Automated citation enforcement for tools, databases, and DOIs
Isolated helper architecture for third-party tool wrappers
Standardized testing protocols using the MYCELIA_RUN_EXTERNAL flag
Reproducibility tracking through version pinning and provenance data

Use Cases

Ensuring all external software and data sources are properly cited for a manuscript
Configuring bioinformatics workflows to run reliably on Linux-based HPC clusters
Integrating new sequence alignment or assembly tools into a multiomic pipeline