MACS3 Remote Tool (MCP Server)

Serves MACS3 (Model-based Analysis of ChIP-Seq; Zhang et al., Genome Biology 2008; the macs3-project Python-3 successor) — the field-standard ChIP-seq / ATAC-seq peak caller — as a ToolUniverse remote tool: run_macs3_callpeak.

Served remotely (not bundled) because it shells out to the macs3 command-line engine (a compiled/Cython dependency) and operates on large server-side alignment files (BAM / BED / BED-PE) rather than inlined data.

run_macs3_callpeak runs macs3 callpeak -t <treatment> [-c <control>] -f <format> -g <genome_size> -n <name> --outdir <tmp> -q <qvalue>, parses the resulting <name>_peaks.narrowPeak (ENCODE BED6+4), and returns the peak count, the top-N peaks by score, and summary statistics.

Deploy

pip install -r requirements.txt   # macs3
python macs3_tool.py              # starts the MCP server on 127.0.0.1:8021

Treatment/control files must be aligned reads in a MACS3-supported format (BAM/BED/SAM, or BAMPE/BEDPE for paired-end such as ATAC-seq). Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse

Tool definition: src/tooluniverse/data/remote_tools/macs3_tools.json (type: RemoteTool). Connect via the standard MCPAutoLoaderTool/server_url mechanism.