File: setup.py

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import os
import shutil
import sys
import glob
from setuptools import setup, find_packages, Extension

#minimap_c_files = [
#    'bseq.c',
#    'index.c',
#    'kthread.c',
#    'map.c',
#    'misc.c',
#    'sdust.c',
#    'sketch.c',
#]
#minimap_c_files = [os.path.join('third_party', 'minimap-0.2', x) for x in minimap_c_files]
minimap_c_files = [os.path.join('ariba', 'ext', 'minimap_ariba.cpp')]
minimap_mod = Extension(
    "minimap_ariba",
    minimap_c_files,
    extra_link_args=['-lz', '-lminimap'],
    include_dirs=[os.path.join(os.path.sep, 'usr', 'include', 'minimap')],
)

#fermilite_c_files = [
#    'bfc.c',
#    'bseq.c',
#    'bubble.c',
#    'htab.c',
#    'ksw.c',
#    'kthread.c',
#    'mag.c',
#    'misc.c',
#    'mrope.c',
#    'rld0.c',
#    'rle.c',
#    'rope.c',
#    'unitig.c'
#]
#fermilite_c_files = [os.path.join('third_party', 'fermi-lite-0.1', x) for x in fermilite_c_files]
fermilite_c_files = [os.path.join('ariba', 'ext', 'fml-asm_ariba.cpp')]
fermilite_mod = Extension(
    "fermilite_ariba",
    fermilite_c_files,
    extra_link_args=['-lz', '-lfml'],
    #include_dirs=[os.path.join('third_party', 'fermi-lite-0.1')],
)

vcfcall_mod = Extension(
    "vcfcall_ariba",
    [os.path.join('ariba', 'ext', 'vcfcall_ariba.cpp')],
)

setup(
    ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
    name='ariba',
    version='2.14.6',
    description='ARIBA: Antibiotic Resistance Identification By Assembly',
    packages = find_packages(),
    package_data={'ariba': ['test_run_data/*',
        'tb_data/*',
        'tests/data/*',
        'tests/data/refdata_query_prepareref/*',
        'tests/data/cluster_test_full_run_ok_non_coding/*',
        'tests/data/cluster_test_full_run_ref_not_in_cluster/*',
        'tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/*',
        'tests/data/ref_preparer_test_run.out/*',
        'tests/data/ref_preparer_test_run_noncoding_checks.out/*',
        'tests/data/clusters_run_with_tb.ref/*',
        'tests/data/cluster_full_run_smtls_snp_varonly_gene/*',
        'tests/data/cluster_test_full_run_delete_codon/*',
        'tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/*',
        'tests/data/cluster_test_full_run_assembly_fail/*',
        'tests/data/cluster_test_full_run_ok_gene_start_mismatch/*',
        'tests/data/cluster_test_full_run_ok_presence_absence/*',
        'tests/data/cluster_test_full_run_multiple_vars/*',
        'tests/data/cluster_full_run_known_smtls_snp_presabs_gene/*',
        'tests/data/cluster_test_full_run_partial_asmbly/*',
        'tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/*',
        'tests/data/cluster_test_init_no_refs_fa/*',
        'tests/data/cluster_full_run_smtls_snp_varonly_gene_2/*',
        'tests/data/cluster_test_full_run_choose_ref_fail/*',
        'tests/data/ref_preparer_test_run_all_noncoding.out/*',
        'tests/data/megares_zip_parser_write_files/*',
        'tests/data/cluster_full_run_smtls_snp_presabs_nonc/*',
        'tests/data/cluster_test_full_run_no_reads_after_filtering/*',
        'tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/*',
        'tests/data/cluster_test_init_no_reads_2/*',
        'tests/data/clusters_load_ref_data_from_dir/*',
        'tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/*',
        'tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/*',
        'tests/data/cluster_test_full_run_ok_variants_only/*',
        'tests/data/cluster_full_run_smtls_snp_varonly_nonc/*',
        'tests/data/cluster_test_full_run_insert_codon/*',
        'tests/data/cluster_test_init_no_reads_1/*',
        'tests/data/cluster_full_run_smtls_snp_presabs_gene/*']},
    author='Martin Hunt',
    author_email='ariba-help@sanger.ac.uk',
    url='https://github.com/sanger-pathogens/ariba',
    scripts=glob.glob('scripts/*'),
    test_suite='nose.collector',
    tests_require=['nose >= 1.3'],
    install_requires=[
        'BeautifulSoup4 >= 4.1.0',
        'biopython',
        'dendropy >= 4.2.0',
        'pyfastaq >= 3.12.0',
        'pysam >= 0.9.1',
        'pymummer<=0.10.3',
        'matplotlib >= 3.1.0',
    ],
    license='GPLv3',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Programming Language :: Python :: 3 :: Only',
        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
    ],
)