Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts, and Python requirements. Use when the user needs to set up a bioinformatics workstation, install tools for a specific assay, create reproducible environments, or troubleshoot dependency issues. Trigger on: install tools, set up environment, conda create, bioinformatics setup, install R packages, install Bioconductor, install pipeline tools.
How to install bioinformatics-installer?
ammawla/encode-toolkit/bioinformatics-installer
$npx -y skills add ammawla/encode-toolkit --skill bioinformatics-installerInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/ammawla/encode-toolkit" --skill "ammawla/encode-toolkit/bioinformatics-installer"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/ammawla/encode-toolkit" that are relevant to the current task. Run `npx skills add "https://github.com/ammawla/encode-toolkit"` and select the relevant skills, then follow their instructions.
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