divref-wf/pixi.toml at main · fg-labs/divref-wf · GitHub

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[workspace]
authors = ["Fulcrum Genomics"]
channels = ["conda-forge", "bioconda"]
name = "fg-labs-divref-wf"
platforms = ["osx-arm64", "osx-64", "linux-64"]
version = "0.1.0"

[feature.snakemake.dependencies]
python = ">=3.12.8,<3.13"
snakemake-minimal = ">=8.28.0,<9.0"
snakefmt = ">=1.0.0,<2"

[pypi-dependencies]
divref = { path = "./divref", editable = true }

[feature.hail.dependencies]
openjdk = ">=11,<17"

[environments]
default = { features = ["snakemake", "hail"] }

[tasks]
check-toolkit = "uv run --directory divref poe check-all"
fix-and-check-toolkit = "uv run --directory divref poe fix-and-check-all"

check-lock   = "pixi lock --check"

check-all = [
    { task = "check-toolkit" },
    { task = "check-lock" },
]

fix-and-check-all = [
    { task = "fix-and-check-toolkit" },
    { task = "check-lock" },
]

setup-gcs = """
python -c "
import os, urllib.request, zipfile, hashlib
jar = os.path.join(__import__('pyspark').__path__[0], 'jars', 'gcs-connector.jar')
expected_sha256 = 'd53cd19ec2fadc3f81319a1dcf3f70940915a674781c29a7067ea6021ae8dfe2'
valid = False
if os.path.exists(jar):
    try:
        zipfile.ZipFile(jar)
        valid = True
    except zipfile.BadZipFile:
        pass
if not valid:
    url = 'https://repo1.maven.org/maven2/com/google/cloud/bigdataoss/gcs-connector/hadoop3-2.2.22/gcs-connector-hadoop3-2.2.22-shaded.jar'
    print(f'Downloading GCS connector JAR to {jar}...')
    urllib.request.urlretrieve(url, jar)
    digest = hashlib.sha256(open(jar, 'rb').read()).hexdigest()
    if digest != expected_sha256:
        raise RuntimeError(f'Checksum mismatch for {jar}: {digest}')
    print('Done.')
else:
    print('GCS connector JAR is already valid.')
"
"""

lint = "snakefmt --line-length 100 workflows/*.smk"
download = "snakemake -j1 -s workflows/download.smk"

[dependencies]
bcftools = ">=1.23.1,<2"