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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 "W2 - Bacterial re-sequencing | Paired-end" from published workflows
workflow_name = "W2 - Bacterial re-sequencing | 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",
"/Whole genome - Escherichia coli/E coli DH10B - Reference",
]
input_labels = [
"Forward Reads",
"Reverse Reads",
"Reference Genome",
]
input_map = {
label: h.import_dataset(get_one(library.get_datasets(name=name))) for name, label in zip(ds_names, input_labels)
}
# Set custom parameters for the "check_contigs" and "sspace" tools
params = {
"check_contigs": {"genomesize": 5.0}, # affects both occurrences
"sspace": {"insert": 300, "error": 0.5, "minoverlap": 35},
}
# 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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