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pyproject.toml
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[build-system]
requires = ["setuptools", "setuptools_scm", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "somaticseq"
keywords = ["somatic mutations", "bioinformatics", "genomics", "ngs"]
authors = [
{name = "Li Tai Fang"},
{name = "Pegah Tootoonchi Afshar"},
{name = "Aparna Chhibber"},
{name = "Marghoob Mohiyuddin"},
{name = "John C. Mu"},
{name = "Greg Gibeling"},
{name = "Sharon Barr"},
{name = "Narges Bani Asadi"},
{name = "Hugo Y.K. Lam"},
]
maintainers = [
{name = "Li Tai Fang", email = "[email protected]"},
]
description = "SomaticSeq: An ensemble approach to accurately detect somatic mutations using SomaticSeq"
readme = "README.md"
requires-python = ">=3.11"
license = {text = "BSD-2-Clause"}
dependencies = [
"pysam",
"numpy",
"scipy",
"pandas",
"xgboost>=1.4",
"pydantic>=2.0.0,<3.0",
]
dynamic = ["version"]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Intended Audience :: Science/Research",
"Intended Audience :: Healthcare Industry",
"Programming Language :: Python :: 3",
]
[project.urls]
Homepage = "https://github.com/bioinform/somaticseq"
[project.scripts]
somaticseq = "somaticseq.somaticseq_parallel:main"
somaticseq_parallel = "somaticseq.somaticseq_parallel:main"
somaticseq_xgboost = "somaticseq.somatic_xgboost:main"
somaticseq_tsv2vcf = "somaticseq.somatic_tsv2vcf:main"
somaticseq_single_vcf2tsv = "somaticseq.single_sample_vcf2tsv:main"
somaticseq_paired_vcf2tsv = "somaticseq.somatic_vcf2tsv:main"
somaticseq_concat = "somaticseq.genomic_file_parsers.concat:main"
somaticseq_linguistic_sequence_complexity = "somaticseq.utilities.linguistic_sequence_complexity:main"
somaticseq_loci_counter = "somaticseq.utilities.lociCounterWithLabels:main"
somaticseq_paired_end_bam2fastq = "somaticseq.utilities.paired_end_bam2fastq:main"
somaticseq_split_bed_into_equal_regions = "somaticseq.utilities.split_bed_into_equal_regions:main"
somaticseq_make_alignment_scripts = "somaticseq.utilities.dockered_pipelines.makeAlignmentScripts:main"
somaticseq_make_somatic_scripts = "somaticseq.utilities.dockered_pipelines.makeSomaticScripts:main"
somaticseq_run_workflows = "somaticseq.utilities.dockered_pipelines.run_workflows:main"
somaticseq_split_vcf = "somaticseq.vcf_modifier.split_vcf:main"
[project.optional-dependencies]
dev = [
"black",
"flake8",
"mypy",
"pytest",
"setuptools_scm",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "--import-mode=importlib"