--- a
+++ b/third_party/nucleus/protos/BUILD
@@ -0,0 +1,401 @@
+load("@com_google_protobuf//:protobuf.bzl", "cc_proto_library", "py_proto_library")
+
+package(default_visibility = [
+    "//visibility:public",
+])
+
+licenses(["notice"])
+
+exports_files(["LICENSE"])
+
+# ----------------------------------------------------------------------
+# proto_library's
+# ----------------------------------------------------------------------
+
+proto_library(
+    name = "bed_proto",
+    srcs = [
+        "bed.proto",
+    ],
+)
+
+proto_library(
+    name = "bedgraph_proto",
+    srcs = [
+        "bedgraph.proto",
+    ],
+)
+
+proto_library(
+    name = "cigar_proto",
+    srcs = ["cigar.proto"],
+)
+
+proto_library(
+    name = "fasta_proto",
+    srcs = [
+        "fasta.proto",
+    ],
+    deps = [
+        ":range_proto",  # NO COPYBARA
+        ":reference_proto",  # NO COPYBARA
+    ],
+)
+
+proto_library(
+    name = "fastq_proto",
+    srcs = [
+        "fastq.proto",
+    ],
+)
+
+proto_library(
+    name = "gff_proto",
+    srcs = [
+        "gff.proto",
+    ],
+    deps = [":range_proto"],  # NO COPYBARA
+)
+
+proto_library(
+    name = "position_proto",
+    srcs = ["position.proto"],
+)
+
+proto_library(
+    name = "range_proto",
+    srcs = ["range.proto"],
+)
+
+proto_library(
+    name = "reads_proto",
+    srcs = [
+        "reads.proto",
+    ],
+    deps = [
+        ":cigar_proto",  # NO COPYBARA
+        ":position_proto",  # NO COPYBARA
+        ":reference_proto",  # NO COPYBARA
+        ":struct_proto",  # NO COPYBARA
+    ],
+)
+
+proto_library(
+    name = "reference_proto",
+    srcs = [
+        "reference.proto",
+    ],
+    deps = [
+        ":range_proto",  # NO COPYBARA
+    ],
+)
+
+proto_library(
+    name = "struct_proto",
+    srcs = ["struct.proto"],
+)
+
+proto_library(
+    name = "variants_proto",
+    srcs = [
+        "variants.proto",
+    ],
+    deps = [
+        ":reference_proto",  # NO COPYBARA
+        ":struct_proto",  # NO COPYBARA
+    ],
+)
+
+proto_library(
+    name = "feature_proto",
+    srcs = ["feature.proto"],
+)
+
+proto_library(
+    name = "example_proto",
+    srcs = ["feature.proto"],
+    deps = [
+        ":feature_proto",  # NO COPYBARA
+    ],
+)
+
+# ----------------------------------------------------------------------
+# cc_proto_library's
+# ----------------------------------------------------------------------
+
+# TODO: Consider definining some new .bzl rules to reduce the
+# boilerplate in these cc_proto_library rules and in this file in general.
+
+cc_proto_library(
+    name = "bed_cc_pb2",
+    srcs = ["bed.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "bedgraph_cc_pb2",
+    srcs = ["bedgraph.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "cigar_cc_pb2",
+    srcs = ["cigar.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "fasta_cc_pb2",
+    srcs = ["fasta.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+    deps = [
+        ":range_cc_pb2",
+        ":reference_cc_pb2",
+    ],
+)
+
+cc_proto_library(
+    name = "fastq_cc_pb2",
+    srcs = ["fastq.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "gff_cc_pb2",
+    srcs = ["gff.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+    deps = [":range_cc_pb2"],
+)
+
+cc_proto_library(
+    name = "position_cc_pb2",
+    srcs = ["position.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "range_cc_pb2",
+    srcs = ["range.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "reads_cc_pb2",
+    srcs = ["reads.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+    deps = [
+        ":cigar_cc_pb2",
+        ":position_cc_pb2",
+        ":reference_cc_pb2",
+        ":struct_cc_pb2",
+    ],
+)
+
+cc_proto_library(
+    name = "reference_cc_pb2",
+    srcs = ["reference.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+    deps = [
+        ":range_cc_pb2",
+    ],
+)
+
+cc_proto_library(
+    name = "struct_cc_pb2",
+    srcs = ["struct.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "variants_cc_pb2",
+    srcs = ["variants.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+    deps = [
+        ":reference_cc_pb2",
+        ":struct_cc_pb2",
+    ],
+)
+
+cc_proto_library(
+    name = "feature_cc_pb2",
+    srcs = ["feature.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+)
+
+cc_proto_library(
+    name = "example_cc_pb2",
+    srcs = ["example.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf",
+    protoc = "@com_google_protobuf//:protoc",
+    deps = [
+        ":feature_cc_pb2",
+    ],
+)
+
+cc_library(
+    name = "all_nucleus_protos_cc",
+    deps = [
+        ":bed_cc_pb2",
+        ":bedgraph_cc_pb2",
+        ":cigar_cc_pb2",
+        ":fasta_cc_pb2",
+        ":fastq_cc_pb2",
+        ":gff_cc_pb2",
+        ":position_cc_pb2",
+        ":range_cc_pb2",
+        ":reads_cc_pb2",
+        ":reference_cc_pb2",
+        ":struct_cc_pb2",
+        ":variants_cc_pb2",
+    ],
+)
+
+# ----------------------------------------------------------------------
+# py_proto_library's
+# ----------------------------------------------------------------------
+
+py_proto_library(
+    name = "bed_py_pb2",
+    srcs = ["bed.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "bedgraph_py_pb2",
+    srcs = ["bedgraph.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "cigar_py_pb2",
+    srcs = ["cigar.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "gff_py_pb2",
+    srcs = ["gff.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+    deps = [":range_py_pb2"],
+)
+
+py_proto_library(
+    name = "fasta_py_pb2",
+    srcs = ["fasta.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+    deps = [
+        ":range_py_pb2",
+        ":reference_py_pb2",
+    ],
+)
+
+py_proto_library(
+    name = "fastq_py_pb2",
+    srcs = ["fastq.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "position_py_pb2",
+    srcs = ["position.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "range_py_pb2",
+    srcs = ["range.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "reads_py_pb2",
+    srcs = ["reads.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+    deps = [
+        ":cigar_py_pb2",
+        ":position_py_pb2",
+        ":reference_py_pb2",
+        ":struct_py_pb2",
+    ],
+)
+
+py_proto_library(
+    name = "reference_py_pb2",
+    srcs = ["reference.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+    deps = [
+        ":range_py_pb2",
+    ],
+)
+
+py_proto_library(
+    name = "struct_py_pb2",
+    srcs = ["struct.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "variants_py_pb2",
+    srcs = ["variants.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+    deps = [
+        ":reference_py_pb2",
+        ":struct_py_pb2",
+    ],
+)
+
+py_proto_library(
+    name = "feature_py_pb2",
+    srcs = ["feature.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+)
+
+py_proto_library(
+    name = "example_py_pb2",
+    srcs = ["example.proto"],
+    default_runtime = "@com_google_protobuf//:protobuf_python",
+    protoc = "@com_google_protobuf//:protoc",
+    py_libs = ["//third_party/nucleus:__init__py"],
+    deps = [
+        ":feature_py_pb2",
+    ],
+)