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from pathlib import Path
from typing import Optional, List, Union
import os
from mcp.server.fastmcp import FastMCP
SERVER_NAME = 'local_bactopia'
mcp = FastMCP(SERVER_NAME)
@mcp.tool()
def bactopia_run(
sample: str,
outdir: str,
datasets: str,
r1: Optional[str] = None,
r2: Optional[str] = None,
se: Optional[str] = None,
fastqs: Optional[str] = None,
accession: Optional[str] = None,
accessions: Optional[str] = None,
profile: str = "conda",
cpus: int = 2,
max_memory: int = 8,
resume: bool = False,
) -> dict:
"""
Run the main Bactopia analysis pipeline for a bacterial genome.
Args:
sample: Name of the sample.
outdir: Directory to store output results.
datasets: Path to the Bactopia datasets directory.
r1: Path to forward reads (Paired-end).
r2: Path to reverse reads (Paired-end).
se: Path to single-end reads.
fastqs: Path to a FOFN (file-of-filenames) for multiple samples.
accession: A single ENA/SRA accession (e.g., SRX000000).
accessions: A file containing a list of ENA/SRA accessions.
profile: Nextflow profile to use (e.g., conda, docker, singularity).
cpus: Number of CPUs to allocate.
max_memory: Maximum memory in GB to allocate.
resume: Whether to resume a previous run.
"""
# Input validation
out_path = Path(outdir)
ds_path = Path(datasets)
if not ds_path.exists():
return {"error": f"Datasets directory not found at {datasets}"}
cmd = ["bactopia", "--sample", sample, "--outdir", str(out_path), "--datasets", str(ds_path)]
# Input source logic
if r1 and r2:
if not Path(r1).exists() or not Path(r2).exists():
return {"error": "R1 or R2 file does not exist"}
cmd += ["--R1", r1, "--R2", r2]
elif se:
if not Path(se).exists():
return {"error": "Single-end file does not exist"}
cmd += ["--SE", se]
elif fastqs:
if not Path(fastqs).exists():
return {"error": "Fastqs list file does not exist"}
cmd += ["--fastqs", fastqs]
elif accession:
cmd += ["--accession", accession]
elif accessions:
if not Path(accessions).exists():
return {"error": "Accessions list file does not exist"}
cmd += ["--accessions", accessions]
else:
return {"error": "No input source provided (R1/R2, SE, fastqs, accession, or accessions required)"}
# Performance and Nextflow options
cmd += ["-profile", profile]
cmd += ["--max_cpus", str(cpus)]
cmd += ["--max_memory", f"{max_memory}.GB"]
if resume:
cmd.append("-resume")
try:
result = subprocess.run(cmd, capture_output=True, text=True, check=True)
return {
"command_executed": " ".join(cmd),
"stdout": result.stdout,
"stderr": result.stderr,
"output_directory": str(out_path.absolute())
}
except subprocess.CalledProcessError as e:
return {
"command_executed": " ".join(cmd),
"error": str(e),
"stdout": e.stdout,
"stderr": e.stderr
}
@mcp.tool()
def bactopia_prepare(
path: str,
recursive: bool = False,
extension: str = ".fastq.gz",
output_file: Optional[str] = None
) -> dict:
"""
Prepare a FASTQ list (FOFN) for Bactopia from a directory of sequencing files.
Args:
path: Directory containing FASTQ files.
recursive: Search for FASTQs in subdirectories.
extension: File extension to look for.
output_file: Optional path to save the generated list.
"""
input_path = Path(path)
if not input_path.is_dir():
return {"error": f"Path {path} is not a directory"}
cmd = ["bactopia", "prepare", str(input_path), "--extension", extension]
if recursive:
cmd.append("--recursive")
try:
result = subprocess.run(cmd, capture_output=True, text=True, check=True)
if output_file:
out_p = Path(output_file)
out_p.write_text(result.stdout)
return {
"command_executed": " ".join(cmd),
"stdout": "File list generated and saved.",
"output_file": str(out_p.absolute())
}
return {
"command_executed": " ".join(cmd),
"stdout": result.stdout,
"stderr": result.stderr
}
except subprocess.CalledProcessError as e:
return {
"command_executed": " ".join(cmd),
"error": str(e),
"stdout": e.stdout,
"stderr": e.stderr
}
@mcp.tool()
def bactopia_search(
query: str,
limit: int = 10,
output_file: Optional[str] = None
) -> dict:
"""
Search for bacterial genome accessions in ENA/SRA.
Args:
query: Search query (e.g., "Staphylococcus aureus").
limit: Maximum number of results to return.
output_file: Optional path to save the accession list.
"""
cmd = ["bactopia", "search", query, "--limit", str(limit)]
try:
result = subprocess.run(cmd, capture_output=True, text=True, check=True)
if output_file:
out_p = Path(output_file)
out_p.write_text(result.stdout)
return {
"command_executed": " ".join(cmd),
"stdout": f"Search results saved to {output_file}",
"output_file": str(out_p.absolute())
}
return {
"command_executed": " ".join(cmd),
"stdout": result.stdout,
"stderr": result.stderr
}
except subprocess.CalledProcessError as e:
return {
"command_executed": " ".join(cmd),
"error": str(e),
"stdout": e.stdout,
"stderr": e.stderr
}
@mcp.tool()
def bactopia_datasets(
outdir: str,
species: Optional[str] = None,
include_genus: bool = False,
limit: int = 100
) -> dict:
"""
Download and setup Bactopia datasets/databases.
Args:
outdir: Directory to save the datasets.
species: Optional species name to download specific datasets (e.g., "Salmonella enterica").
include_genus: Include genus-level datasets.
limit: Limit the number of genomes used for building datasets.
"""
out_path = Path(outdir)
cmd = ["bactopia", "datasets", "--outdir", str(out_path)]
if species:
cmd += ["--species", species]
if include_genus:
cmd.append("--include_genus")
cmd += ["--limit", str(limit)]
try:
# This can be a long-running process
result = subprocess.run(cmd, capture_output=True, text=True, check=True)
return {
"command_executed": " ".join(cmd),
"stdout": result.stdout,
"stderr": result.stderr,
"datasets_path": str(out_path.absolute())
}
except subprocess.CalledProcessError as e:
return {
"command_executed": " ".join(cmd),
"error": str(e),
"stdout": e.stdout,
"stderr": e.stderr
}
@mcp.tool()
def bactopia_tool(
tool_name: str,
bactopia_dir: str,
outdir: str,
profile: str = "conda",
cpus: int = 2,
extra_params: Optional[List[str]] = None
) -> dict:
"""
Run a Bactopia Tool (comparative analysis) on existing Bactopia outputs.
Common tools include: pangenome, roary, iqtree, pirate, summary, etc.
Args:
tool_name: Name of the Bactopia Tool to run.
bactopia_dir: Directory containing previous Bactopia results.
outdir: Directory to store tool results.
profile: Nextflow profile to use.
cpus: Number of CPUs to allocate.
extra_params: List of additional command line arguments for the specific tool.
"""
b_path = Path(bactopia_dir)
o_path = Path(outdir)
if not b_path.exists():
return {"error": f"Bactopia results directory not found at {bactopia_dir}"}
cmd = [
"bactopia", tool_name,
"--bactopia", str(b_path),
"--outdir", str(o_path),
"-profile", profile,
"--max_cpus", str(cpus)
]
if extra_params:
cmd.extend(extra_params)
try:
result = subprocess.run(cmd, capture_output=True, text=True, check=True)
return {
"command_executed": " ".join(cmd),
"stdout": result.stdout,
"stderr": result.stderr,
"output_directory": str(o_path.absolute())
}
except subprocess.CalledProcessError as e:
return {
"command_executed": " ".join(cmd),
"error": str(e),
"stdout": e.stdout,
"stderr": e.stderr
}
if __name__ == "__main__":
mcp.run(transport="stdio")
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