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setup.py
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setup.py
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#!/usr/bin/env python3
from setuptools import find_packages, setup
from somaticseq._version import __version__
print(__version__)
with open("README.md") as fn:
long_description = fn.read()
setup(
name="somaticseq",
version=__version__,
description="SomaticSeq: An ensemble approach to accurately detect somatic mutations using SomaticSeq",
long_description=long_description,
long_description_content_type="text/markdown",
author="Li Tai Fang",
author_email="ltfang@gmail.com",
url="https://github.com/bioinform/somaticseq",
packages=find_packages(),
package_data={"": ["*.R"]},
python_requires=">=3.10.0",
install_requires=[
"pysam",
"numpy",
"scipy",
"pandas",
"xgboost>=1.4,<2.0",
"pydantic>=2.0.0,<3.0",
],
scripts=[
"somaticseq/somaticseq_parallel.py",
"somaticseq/run_somaticseq.py",
"somaticseq/single_sample_vcf2tsv.py",
"somaticseq/somatic_vcf2tsv.py",
"somaticseq/somatic_xgboost.py",
"somaticseq/somatic_tsv2vcf.py",
"somaticseq/genomic_file_parsers/concat.py",
"somaticseq/utilities/linguistic_sequence_complexity.py",
"somaticseq/utilities/lociCounterWithLabels.py",
"somaticseq/utilities/paired_end_bam2fastq.py",
"somaticseq/utilities/remove_callers_from_somaticseq_tsv.py",
"somaticseq/utilities/split_bed_into_equal_regions.py",
"somaticseq/utilities/tally_variants_from_multiple_vcfs.py",
"somaticseq/utilities/variant_annotation.py",
"somaticseq/utilities/vcfsorter.pl",
"somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py",
"somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py",
"somaticseq/utilities/dockered_pipelines/run_workflows.py",
"somaticseq/vcf_modifier/splitVcf.py",
"r_scripts/ada_model_builder_ntChange.R",
"r_scripts/ada_model_predictor.R",
],
)