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import json
import os
import sys
from common import get_one # noqa:I100,I201
from bioblend.galaxy.objects import GalaxyInstance
URL = "https://orione.crs4.it"
API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
if API_KEY == "YOUR_API_KEY":
sys.exit("API_KEY not set, see the README.txt file")
gi = GalaxyInstance(URL, API_KEY)
# Select "W5 - Metagenomics" from published workflows
workflow_name = "W5 - Metagenomics"
previews = gi.workflows.get_previews(name=workflow_name, published=True)
p = get_one(_ for _ in previews if _.published)
# Import the workflow to user space
iw = gi.workflows.import_shared(p.id)
# Create a new history
history_name = f"{workflow_name} output"
h = gi.histories.create(history_name)
# Select the "Orione SupMat" library
library_name = "Orione SupMat"
library = get_one(gi.libraries.list(name=library_name))
# Select the "/Metagenomics/MetagenomicsDataset.fq" dataset
ds_name = "/Metagenomics/MetagenomicsDataset.fq"
input_map = {"Input Dataset": h.import_dataset(get_one(library.get_datasets(name=ds_name)))}
# Select the blastn step
tool_id = "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00"
step_id = get_one(iw.tool_labels_to_ids[tool_id])
ws = iw.steps[step_id]
# Get (a copy of) the parameters dict for the selected step
ws_parameters = ws.tool_inputs.copy()
# Run the workflow on a new history with the selected dataset
# as input, setting the BLAST db to "16SMicrobial-20131106"
params = {tool_id: {"db_opts": json.loads(ws_parameters["db_opts"])}}
params[tool_id]["db_opts"]["database"] = "16SMicrobial-20131106"
outputs, out_hist = iw.run(input_map, h, params=params)
assert out_hist.name == history_name
print(f"Running workflow: {iw.name} [{iw.id}]")
print(f"Output history: {out_hist.name} [{out_hist.id}]")
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