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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 "W3 - Bacterial de novo assembly | Paired-end" from published workflows
workflow_name = "W3 - Bacterial de novo assembly | Paired-end"
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 datasets
ds_names = [
"/Whole genome - Escherichia coli/E coli DH10B MiSeq R1.fastq",
"/Whole genome - Escherichia coli/E coli DH10B MiSeq R2.fastq",
]
input_labels = [
"Left/Forward FASTQ Reads",
"Right/Reverse FASTQ Reads",
]
input_map = {
label: h.import_dataset(get_one(library.get_datasets(name=name))) for name, label in zip(ds_names, input_labels)
}
# Set the "hash_length" parameter to different values for the 3 "velveth" steps
lengths = {"19", "23", "29"}
ws_ids = iw.tool_labels_to_ids["velveth"]
assert len(ws_ids) == len(lengths)
params = {id_: {"hash_length": v} for id_, v in zip(ws_ids, lengths)}
# Set the "ins_length" runtime parameter to the same value for the 3
# "velvetg" steps
tool_id = "velvetg"
ws_ids = iw.tool_labels_to_ids[tool_id]
step = iw.steps[next(iter(ws_ids))] # arbitrarily pick one
params[tool_id] = {"reads": json.loads(step.tool_inputs["reads"]).copy()}
params[tool_id]["reads"]["ins_length"] = -1
# Set more custom parameters
params["cisarunner"] = {"genomesize": 5000000}
params["check_contigs"] = {"genomesize": 5.0}
params["toolshed.g2.bx.psu.edu/repos/edward-kirton/abyss_toolsuite/abyss/1.0.0"] = {"k": 41}
# Run the workflow on a new history with the selected datasets as inputs
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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