--- a
+++ b/WORKSPACE
@@ -0,0 +1,181 @@
+# The workspace name appears at the top of the runfiles tree,
+# and in paths to tests, so to keep python happy it is best
+# if it is unique.
+workspace(name = "com_google_deepvariant")
+
+load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
+
+# Note: absl_py and com_google_absl (the Python and C++ abseil libraries) are
+# provided by TensorFlow.
+
+# CCTZ (Time-zone framework).
+# TODO: transitive WORKSPACE dependency resolution doesn't
+# work in bazel, so we need to include this to enable nucleus's use of
+# //absl/{time,synchronization}
+http_archive(
+    name = "com_googlesource_code_cctz",
+    strip_prefix = "cctz-master",
+    urls = ["https://github.com/google/cctz/archive/master.zip"],
+)
+
+# This is the 1.18 release of htslib.
+http_archive(
+    name = "htslib",
+    build_file = "//:third_party/htslib.BUILD",
+    sha256 = "f1ab53a593a2320a1bfadf4ef915dae784006c5b5c922c8a8174d7530a9af18f",
+    strip_prefix = "htslib-1.18",
+    urls = [
+        "https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2",
+    ],
+)
+
+http_archive(
+    name = "libssw",
+    build_file = "//:third_party/libssw.BUILD",
+    sha256 = "b294c0cb6f0f3d578db11b4112a88b20583b9d4190b0a9cf04d83bb6a8704d9a",
+    # Note: HHBlits requires a patch (internal) in ssw_align to work.
+    strip_prefix = "Complete-Striped-Smith-Waterman-Library-1.2.5",
+    urls = [
+        "https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive/v1.2.5.tar.gz",
+    ],
+)
+
+http_archive(
+    name = "gbwt",
+    build_file = "//:third_party/gbwt.BUILD",
+    sha256 = "21d3679349ef9809a886da50f0a2036eba0c172b97826a7882322f81649397e2",
+    strip_prefix = "gbwt-0b3aacbea6f7d285a3c5fbd0a22b4aa2ac8957d6",
+    urls = [
+        "https://github.com/mobinasri/gbwt/archive/0b3aacbea6f7d285a3c5fbd0a22b4aa2ac8957d6.zip",
+    ],
+)
+
+http_archive(
+    name = "libhandlegraph",
+    build_file = "//:third_party/libhandlegraph.BUILD",
+    sha256 = "078dee9ab07996193117b54d75f6e4cfd881851da5e3c3e3d8c669c7eefeaaa2",
+    strip_prefix = "libhandlegraph-b2fc22c552440076b340306fc660b4fa309fb005",
+    urls = [
+        "https://github.com/mobinasri/libhandlegraph/archive/b2fc22c552440076b340306fc660b4fa309fb005.zip",
+    ],
+)
+
+http_archive(
+    name = "sdsl_lite",
+    build_file = "//:third_party/sdsl_lite.BUILD",
+    sha256 = "24c454fae9f2b4e5d20ce7df9817027e1315bef2eca519e0f123a0b970b757d2",
+    strip_prefix = "sdsl_lite-4cb63b65854983bec395d799aaff342bd0cc376f",
+    urls = [
+        "https://github.com/mobinasri/sdsl_lite/archive/4cb63b65854983bec395d799aaff342bd0cc376f.zip",
+    ],
+)
+
+http_archive(
+    name = "gbwtgraph",
+    build_file = "//:third_party/gbwtgraph.BUILD",
+    sha256 = "40c41c34b152a1eea6991e1acfdad8875e0c738e24cd36ca22dab5187c99a910",
+    strip_prefix = "gbwtgraph-c96ca88b65fc40ac4bd371319a29111015d38904",
+    urls = [
+        "https://github.com/mobinasri/gbwtgraph/archive/c96ca88b65fc40ac4bd371319a29111015d38904.zip",
+    ],
+)
+
+http_archive(
+    name = "libdivsufsort",
+    build_file = "//:third_party/libdivsufsort.BUILD",
+    sha256 = "6a94e0ae99824b027a732062fab2ebd16091ada33ba1b90ba0e9892f2afec8b8",
+    strip_prefix = "libdivsufsort-22e6b23e619ff50fd086844b6e618d53ca9d53bd",
+    urls = [
+        "https://github.com/simongog/libdivsufsort/archive/22e6b23e619ff50fd086844b6e618d53ca9d53bd.zip",
+    ],
+)
+
+# Import tensorflow.  Note path.
+local_repository(
+    name = "org_tensorflow",
+    path = "../tensorflow",
+)
+
+# Required boilerplate for tf_workspace().
+# This is copied from https://github.com/tensorflow/tensorflow/blob/v2.3.0/WORKSPACE.
+http_archive(
+    name = "io_bazel_rules_closure",
+    sha256 = "5b00383d08dd71f28503736db0500b6fb4dda47489ff5fc6bed42557c07c6ba9",
+    strip_prefix = "rules_closure-308b05b2419edb5c8ee0471b67a40403df940149",
+    urls = [
+        "https://storage.googleapis.com/mirror.tensorflow.org/github.com/bazelbuild/rules_closure/archive/308b05b2419edb5c8ee0471b67a40403df940149.tar.gz",
+        "https://github.com/bazelbuild/rules_closure/archive/308b05b2419edb5c8ee0471b67a40403df940149.tar.gz",  # 2019-06-13
+    ],
+)
+
+# This needs to be in sync with the version of protobuf used by TensorFlow,
+# which is currently defined in @tensorflow/tensorflow/workspace.bzl.
+# We supply our own BUILD file, though, so we can prevent ODR violations by
+# putting all of Nucleus's C++ binary dependencies into a single library.
+# That BUILD file must be kept in sync with the version of protobuf used.
+http_archive(
+    name = "com_google_protobuf",
+    build_file = "//:third_party/protobuf.BUILD",
+    patch_args = ["-p1"],
+    patches = ["//:third_party/protobuf.patch"],
+    sha256 = "cfcba2df10feec52a84208693937c17a4b5df7775e1635c1e3baffc487b24c9b",
+    # This protobuf release is based on protobuf 3.9.2.
+    strip_prefix = "protobuf-3.9.2",
+    urls = [
+        "https://storage.googleapis.com/mirror.tensorflow.org/github.com/protocolbuffers/protobuf/archive/v3.9.2.zip",
+        "https://github.com/protocolbuffers/protobuf/archive/v3.9.2.zip",
+    ],
+)
+
+http_archive(
+    name = "com_google_glog",
+    sha256 = "1ee310e5d0a19b9d584a855000434bb724aa744745d5b8ab1855c85bff8a8e21",
+    strip_prefix = "glog-028d37889a1e80e8a07da1b8945ac706259e5fd8",
+    urls = [
+        "https://mirror.bazel.build/github.com/google/glog/archive/028d37889a1e80e8a07da1b8945ac706259e5fd8.tar.gz",
+        "https://github.com/google/glog/archive/028d37889a1e80e8a07da1b8945ac706259e5fd8.tar.gz",
+    ],
+)
+
+# bazel_skylib is now a required dependency of protobuf_archive.
+http_archive(
+    name = "bazel_skylib",
+    sha256 = "74d544d96f4a5bb630d465ca8bbcfe231e3594e5aae57e1edbf17a6eb3ca2506",
+    urls = [
+        "https://mirror.bazel.build/github.com/bazelbuild/bazel-skylib/releases/download/1.3.0/bazel-skylib-1.3.0.tar.gz",
+        "https://github.com/bazelbuild/bazel-skylib/releases/download/1.3.0/bazel-skylib-1.3.0.tar.gz",
+    ],
+)
+
+http_archive(
+    name = "pybind11_protobuf",
+    sha256 = "21e0c32d81ece8039a3a8e6daafbd7f64cb0c2744492f3b00f11baa0e276d1a5",
+    strip_prefix = "pybind11_protobuf-de94308491982c32ddfe305a5dfc3c38bc9ff2bc",
+    urls = [
+        "https://github.com/pichuan/pybind11_protobuf/archive/de94308491982c32ddfe305a5dfc3c38bc9ff2bc.zip",
+    ],
+)
+
+# Import all of the tensorflow dependencies.
+# Copied from tensorflow/WORKSPACE. Updated in v2.5.0:
+load("@org_tensorflow//tensorflow:workspace3.bzl", "tf_workspace3")
+
+tf_workspace3()
+
+load("@org_tensorflow//tensorflow:workspace2.bzl", "tf_workspace2")
+
+tf_workspace2()
+
+load("@org_tensorflow//tensorflow:workspace1.bzl", "tf_workspace1")
+
+tf_workspace1()
+
+load("@org_tensorflow//tensorflow:workspace0.bzl", "tf_workspace0")
+
+tf_workspace0()
+
+new_local_repository(
+    name = "clif",
+    build_file = "third_party/clif.BUILD",
+    path = "/usr/local",
+)