1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
|
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')],
)
with open("requirements.txt") as f:
install_requires = [x.rstrip() for x in f]
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',
url='https://github.com/sanger-pathogens/ariba',
scripts=glob.glob('scripts/*'),
test_suite='nose.collector',
tests_require=['nose >= 1.3'],
install_requires=install_requires,
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)',
],
)
|
