Update run_deepvariant with savedmodel paths

PiperOrigin-RevId: 570145106
yinshiyi · Oct 2, 2023 · d05b868 · d05b868
1 parent 53f48c9
commit d05b868
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -181,14 +181,14 @@ ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.pacbio.rc1.savedmodel/variables/variables.index .
 RUN chmod +r /opt/models/pacbio/*
 
-WORKDIR /opt/models/hybrid
+WORKDIR /opt/models/hybrid_pacbio_illumina
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.hybrid.rc1.savedmodel/fingerprint.pb .
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.hybrid.rc1.savedmodel/saved_model.pb .
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.hybrid.rc1.savedmodel/example_info.json .
-WORKDIR /opt/models/hybrid/variables
+WORKDIR /opt/models/hybrid_pacbio_illumina/variables
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.hybrid.rc1.savedmodel/variables/variables.data-00000-of-00001 .
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.hybrid.rc1.savedmodel/variables/variables.index .
-RUN chmod +r /opt/models/hybrid/*
+RUN chmod +r /opt/models/hybrid_pacbio_illumina/*
 
 WORKDIR /opt/models/ont_r104
 ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION}/rc1_savedmodels/deepvariant.ont.rc1.savedmodel/fingerprint.pb .

diff --git a/deepvariant/scripts/run_deepvariant.py b/deepvariant/scripts/run_deepvariant.py
@@ -245,16 +245,16 @@
 
 
 MODEL_TYPE_MAP = {
-    'WGS': '/opt/models/wgs/model.ckpt',
-    'WES': '/opt/models/wes/model.ckpt',
-    'PACBIO': '/opt/models/pacbio/model.ckpt',
-    'ONT_R104': '/opt/models/ont_r104/model.ckpt',
-    'HYBRID_PACBIO_ILLUMINA': '/opt/models/hybrid_pacbio_illumina/model.ckpt',
+    'WGS': '/opt/models/wgs',
+    'WES': '/opt/models/wes',
+    'PACBIO': '/opt/models/pacbio',
+    'ONT_R104': '/opt/models/ont_r104',
+    'HYBRID_PACBIO_ILLUMINA': '/opt/models/hybrid_pacbio_illumina',
 }
 
 # Current release version of DeepVariant.
 # Should be the same in dv_vcf_constants.py.
-DEEP_VARIANT_VERSION = '1.5.0'
+DEEP_VARIANT_VERSION = '1.6.0'
 
 
 def _is_quoted(value):

diff --git a/deepvariant/scripts/run_deepvariant_test.py b/deepvariant/scripts/run_deepvariant_test.py
@@ -90,7 +90,7 @@ def test_basic_commands(self, model_type, use_slim_model):
         '--outfile '
         '"/tmp/deepvariant_tmp_output/call_variants_output.tfrecord.gz" '
         '--examples "/tmp/deepvariant_tmp_output/[email protected]" '
-        '--checkpoint "/opt/models/{}/model.ckpt"'.format(
+        '--checkpoint "/opt/models/{}"'.format(
             call_variants_bin, model_type.lower()
         ),
     )
@@ -156,7 +156,7 @@ def test_pacbio_basic_commands(self):
             ' "/tmp/deepvariant_tmp_output/call_variants_output.tfrecord.gz"'
             ' --examples'
             ' "/tmp/deepvariant_tmp_output/[email protected]"'
-            ' --checkpoint "/opt/models/pacbio/model.ckpt"'
+            ' --checkpoint "/opt/models/pacbio"'
         ),
     )
     self.assertEqual(
@@ -222,7 +222,7 @@ def test_ont_basic_commands(self):
             ' "/tmp/deepvariant_tmp_output/call_variants_output.tfrecord.gz"'
             ' --examples'
             ' "/tmp/deepvariant_tmp_output/[email protected]"'
-            ' --checkpoint "/opt/models/ont_r104/model.ckpt"'
+            ' --checkpoint "/opt/models/ont_r104"'
         ),
     )
     self.assertEqual(
@@ -275,7 +275,7 @@ def test_sample_name_command(self, sample_name):
             ' "/tmp/deepvariant_tmp_output/call_variants_output.tfrecord.gz"'
             ' --examples'
             ' "/tmp/deepvariant_tmp_output/[email protected]"'
-            ' --checkpoint "/opt/models/wgs/model.ckpt"'
+            ' --checkpoint "/opt/models/wgs"'
         ),
     )
     self.assertEqual(
@@ -677,7 +677,7 @@ def test_call_variants_extra_args(
         '--outfile '
         '"/tmp/deepvariant_tmp_output/call_variants_output.tfrecord.gz" '
         '--examples "/tmp/deepvariant_tmp_output/[email protected]" '
-        '--checkpoint "/opt/models/wgs/model.ckpt" '
+        '--checkpoint "/opt/models/wgs" '
         '%s' % expected_args,
     )