|
a |
|
b/BUILD |
|
|
1 |
load("//third_party/nucleus/tools:zip_dir.bzl", "zip_dir") |
|
|
2 |
|
|
|
3 |
package( |
|
|
4 |
default_visibility = [ |
|
|
5 |
"//visibility:public", |
|
|
6 |
], |
|
|
7 |
) |
|
|
8 |
|
|
|
9 |
test_suite( |
|
|
10 |
name = "smoke_tests", |
|
|
11 |
tests = [ |
|
|
12 |
"//deepvariant/core:smoke_tests", |
|
|
13 |
"//deepvariant/environment_tests:smoke_tests", |
|
|
14 |
"//deepvariant/testing:smoke_tests", |
|
|
15 |
], |
|
|
16 |
) |
|
|
17 |
|
|
|
18 |
filegroup( |
|
|
19 |
name = "binaries", |
|
|
20 |
srcs = [ |
|
|
21 |
"//deepvariant:binaries", |
|
|
22 |
], |
|
|
23 |
) |
|
|
24 |
|
|
|
25 |
filegroup( |
|
|
26 |
name = "binaries-deeptrio", |
|
|
27 |
srcs = [ |
|
|
28 |
"//deeptrio:binaries", |
|
|
29 |
], |
|
|
30 |
) |
|
|
31 |
|
|
|
32 |
exports_files(["LICENSE"]) |
|
|
33 |
|
|
|
34 |
filegroup( |
|
|
35 |
name = "licenses", |
|
|
36 |
srcs = [ |
|
|
37 |
":LICENSE", |
|
|
38 |
"//third_party:abseil_cpp.LICENSE", # TODO |
|
|
39 |
"//third_party:boost.LICENSE", |
|
|
40 |
"@com_google_protobuf//:LICENSE", |
|
|
41 |
"@com_googlesource_code_re2//:LICENSE", |
|
|
42 |
"@gbwt//:LICENSE", |
|
|
43 |
"@gbwtgraph//:LICENSE", |
|
|
44 |
"@htslib//:LICENSE", |
|
|
45 |
"@libdivsufsort//:LICENSE", |
|
|
46 |
"@libssw//:README.md", # SSW license embedded in the README. |
|
|
47 |
"@org_tensorflow//:LICENSE", |
|
|
48 |
"@sdsl_lite//:COPYING", |
|
|
49 |
], |
|
|
50 |
) |
|
|
51 |
|
|
|
52 |
zip_dir( |
|
|
53 |
name = "licenses_zip", |
|
|
54 |
srcs = [":licenses"], |
|
|
55 |
zipname = "licenses.zip", |
|
|
56 |
) |
|
|
57 |
|
|
|
58 |
cc_library( |
|
|
59 |
name = "all_extensions", |
|
|
60 |
srcs = [], |
|
|
61 |
deps = [ |
|
|
62 |
"//deepvariant/python:allelecounter_cclib", |
|
|
63 |
"//deepvariant/python:direct_phasing_cclib", |
|
|
64 |
"//deepvariant/python:make_examples_native_cclib", |
|
|
65 |
"//deepvariant/python:pileup_image_native_cclib", |
|
|
66 |
"//deepvariant/python:postprocess_variants_cclib", |
|
|
67 |
"//deepvariant/python:variant_calling_cclib", |
|
|
68 |
"//deepvariant/python:variant_calling_multisample_cclib", |
|
|
69 |
"//deepvariant/realigner/python:debruijn_graph_cclib", |
|
|
70 |
"//deepvariant/realigner/python:fast_pass_aligner_cclib", |
|
|
71 |
"//deepvariant/realigner/python:ssw_cclib", |
|
|
72 |
"//deepvariant/realigner/python:window_selector_cclib", |
|
|
73 |
"//third_party/nucleus/core/python:statusor_examples_cclib", |
|
|
74 |
"//third_party/nucleus/io/python:bed_reader_cclib", |
|
|
75 |
"//third_party/nucleus/io/python:bed_writer_cclib", |
|
|
76 |
"//third_party/nucleus/io/python:bedgraph_reader_cclib", |
|
|
77 |
"//third_party/nucleus/io/python:bedgraph_writer_cclib", |
|
|
78 |
"//third_party/nucleus/io/python:fastq_reader_cclib", |
|
|
79 |
"//third_party/nucleus/io/python:fastq_writer_cclib", |
|
|
80 |
"//third_party/nucleus/io/python:gbz_reader_cclib", |
|
|
81 |
"//third_party/nucleus/io/python:gff_reader_cclib", |
|
|
82 |
"//third_party/nucleus/io/python:gff_writer_cclib", |
|
|
83 |
"//third_party/nucleus/io/python:gfile_cclib", |
|
|
84 |
"//third_party/nucleus/io/python:hts_verbose_cclib", |
|
|
85 |
"//third_party/nucleus/io/python:merge_variants_cclib", |
|
|
86 |
"//third_party/nucleus/io/python:reference_cclib", |
|
|
87 |
"//third_party/nucleus/io/python:sam_reader_cclib", |
|
|
88 |
"//third_party/nucleus/io/python:sam_writer_cclib", |
|
|
89 |
"//third_party/nucleus/io/python:tabix_indexer_cclib", |
|
|
90 |
"//third_party/nucleus/io/python:tfrecord_reader_cclib", |
|
|
91 |
"//third_party/nucleus/io/python:tfrecord_writer_cclib", |
|
|
92 |
"//third_party/nucleus/io/python:vcf_concat_cclib", |
|
|
93 |
"//third_party/nucleus/io/python:vcf_reader_cclib", |
|
|
94 |
"//third_party/nucleus/io/python:vcf_writer_cclib", |
|
|
95 |
"//third_party/nucleus/util/python:math_cclib", |
|
|
96 |
"//third_party/nucleus/util/python:utils_cclib", |
|
|
97 |
], |
|
|
98 |
) |
|
|
99 |
|
|
|
100 |
# Until https://github.com/bazelbuild/bazel/issues/4815 is fixed, |
|
|
101 |
# we need to specify and force the use of a py_runtime. |
|
|
102 |
py_runtime( |
|
|
103 |
name = "deepvariant_python_runtime", |
|
|
104 |
files = [], |
|
|
105 |
interpreter_path = select({ |
|
|
106 |
"@bazel_tools//tools/python:PY3": "/usr/bin/python3", |
|
|
107 |
}), |
|
|
108 |
) |