BUILD

load("//nucleus/tools:zip_dir.bzl", "zip_dir")

package(
    default_visibility = [
        "//visibility:public",
    ],
)

# TODO(thomaswc): Add smoke tests for Nucleus.

filegroup(
    name = "libraries",
    srcs = [
        "//nucleus",
        "//nucleus:nucleus_py",
    ],
)

exports_files(["LICENSE"])

filegroup(
    name = "licenses",
    srcs = [
        ":LICENSE",
        "//third_party:abseil_cpp.LICENSE",  # TODO(b/69856150)
        "@com_google_protobuf//:LICENSE",
        "@com_googlesource_code_re2//:LICENSE",
        "@htslib//:LICENSE",
        "@org_tensorflow//:LICENSE",
    ],
)

zip_dir(
    name = "licenses_zip",
    srcs = [":licenses"],
    zipname = "licenses.zip",
)

cc_library(
    name = "all_extensions",
    srcs = [],
    deps = [
        "//nucleus/io/python:bed_reader_cclib",
        "//nucleus/io/python:bed_writer_cclib",
        "//nucleus/io/python:bedgraph_reader_cclib",
        "//nucleus/io/python:bedgraph_writer_cclib",
        "//nucleus/io/python:fastq_reader_cclib",
        "//nucleus/io/python:fastq_writer_cclib",
        "//nucleus/io/python:gff_reader_cclib",
        "//nucleus/io/python:gff_writer_cclib",
        "//nucleus/io/python:gfile_cclib",
        "//nucleus/io/python:hts_verbose_cclib",
        "//nucleus/io/python:reference_cclib",
        "//nucleus/io/python:sam_reader_cclib",
        "//nucleus/io/python:sam_writer_cclib",
        "//nucleus/io/python:tabix_indexer_cclib",
        "//nucleus/io/python:tfrecord_reader_cclib",
        "//nucleus/io/python:tfrecord_writer_cclib",
        "//nucleus/io/python:vcf_reader_cclib",
        "//nucleus/io/python:vcf_writer_cclib",
        "//nucleus/util/python:math_cclib",
        "//nucleus/util/python:utils_cclib",
        "//nucleus/vendor/python:statusor_examples_cclib",
    ],
)

# Until https://github.com/bazelbuild/bazel/issues/4815 is fixed,
# we need to specify and force the use of a py_runtime.
py_runtime(
    name = "nucleus_python_runtime",
    files = [],
    interpreter_path = select({
        "@bazel_tools//tools/python:PY2": "/usr/bin/python2",
        "@bazel_tools//tools/python:PY3": "/usr/bin/python3",
    }),
)