ammawla/encode-toolkit

v0.3.0-beta.9 Feature

This release adds 3 notable features for engineering teams evaluating rollout.

Published 2mo MCP Developer Tools

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✓ No known CVEs patched

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✓ No known CVEs patched in this version

Topics

ai ai-agents ai-bio bioinformatics bioinformatics-tool claude

+9 more

claude-code claude-code-mcp claude-code-plugin claude-code-skills claude-mcp claude-plugin claude-skills encode mcp-server

Summary

AI summary

Adds full Cursor plugin support with manifests, new commands, and pipeline agents.

Full changelog

What's New

Cursor Plugin Compatibility

Install encode-toolkit in Cursor via .cursor-plugin/ manifest:

Full plugin.json + marketplace.json manifests
4 Cursor rules (.mdc): data quality, provenance, API patterns, file formats
MCP server auto-configuration

Commands (10)

Quick-action entry points covering all 20 MCP tools:

search-encode, download-encode, browse-files, track-experiments
quality-check, cite-encode, cross-reference, compare-experiments
manage-credentials, log-provenance

Pipeline Agents (7)

Multi-step pipeline execution agents:

ChIP-seq (BWA-MEM → MACS2 → IDR)
ATAC-seq (Bowtie2 → Tn5 shift → MACS2)
RNA-seq (STAR 2-pass → RSEM → Kallisto)
WGBS (Bismark → MethylDackel)
Hi-C (BWA → pairtools → Juicer → HiCCUPS)
DNase-seq (BWA → Hotspot2 → HINT-ATAC)
CUT&RUN (Bowtie2 → SEACR → spike-in)

Pre-commit Hooks

OS file blocker (.DS_Store, Thumbs.db)
Case conflict and merge conflict detection
Ruff lint + format, mypy, YAML/JSON validation

Housekeeping

.gitignore cleaned up, local-only entries moved to .git/info/exclude
Version 0.3.0-beta.9 across all 8 manifest files

Full Plugin Contents

20 MCP tools (ENCODE API)
47 workflow skills
10 commands
7 pipeline agents
4 Cursor rules
7 Nextflow pipelines
14 database integrations

Full Changelog: https://github.com/ammawla/encode-toolkit/compare/v0.3.0-beta.8...v0.3.0-beta.9

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About ammawla/encode-toolkit

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments.

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