Babraham Bioinformatics FastQC Software Package

This package provides FastQC binaries for the Platforma Backend system.

Reference

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Installation

npm install @platforma-open/babraham.software-fastqc

Usage

The package provides FastQC binaries for various platforms. The binaries are automatically selected based on the host system.

Version Upgrade Instructions

To upgrade to a new version of FastQC:

1. Download the new FastQC version:

   • Go to https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
   • Download the latest version (e.g., fastqc_v0.12.1.zip)

2. Prepare the binaries:

   • Create the dld directory if it doesn't exist:

     mkdir -p dld

   • Extract the downloaded archive to the dld directory:

     unzip fastqc_v0.12.1.zip -d dld/

   • Rename the extracted directory to match the expected structure:

     mv dld/FastQC dld/fastqc

3. Update package.json:

   • Update the version in block-software.entrypoints.main.binary.artifact.version to the new version (e.g., "0.12.1")
   • Bump the package version in the root version field if needed

4. Build and publish:

   npm run pkg:build
   npm run pkg:publish

Note: FastQC is a Java application, so the package includes the Java runtime environment. The build process will handle the necessary Java configuration automatically.

Supported Platforms

• Linux (x64, aarch64)
• macOS (x64, aarch64)
• Windows (x64)

License

UNLICENSED