diff --git a/examples/biosciences/alphagenome/inference.sh b/examples/biosciences/alphagenome/inference.sh
old mode 100644
new mode 100755
index 64c62b214e063833ffe82ff07d70876836832c49..89342b652fa8553c5b8dd03fdd60ae20a4f5920a
--- a/examples/biosciences/alphagenome/inference.sh
+++ b/examples/biosciences/alphagenome/inference.sh
@@ -2,8 +2,8 @@
 
 source ../../../env.sh
 export PYTHONPATH=$(pwd):$PYTHONPATH
-export DATA_ROOT_DIR=${ONESCIENCE_DATASETS_DIR}/AlphaGeonme
-export MODEL_ROOT_DIR=${ONESCIENCE_MODELS_DIR}/AlphaGeonme
+export DATA_ROOT_DIR=${ONESCIENCE_DATASETS_DIR}/AlphaGenome
+export MODEL_ROOT_DIR=${ONESCIENCE_MODELS_DIR}/AlphaGenome
 
 python run_inference.py \
     --fasta_path ${DATA_ROOT_DIR}/reference/HOMO_SAPIENS/GRCh38.p13.genome.fa \
@@ -11,4 +11,4 @@ python run_inference.py \
     --chromosome chr19 \
     --start 10587331 \
     --end 11635907 \
-    --output_dir ./outputs
\ No newline at end of file
+    --output_dir ./outputs
diff --git a/examples/biosciences/alphagenome/run_track.sh b/examples/biosciences/alphagenome/run_track.sh
old mode 100644
new mode 100755
index 17b691441cfac4111915ce21fa00538e1f07072a..a032a4a7678ffae6ad22d26fd0719e3d81b4040b
--- a/examples/biosciences/alphagenome/run_track.sh
+++ b/examples/biosciences/alphagenome/run_track.sh
@@ -2,11 +2,12 @@
 
 source ../../../env.sh
 export PYTHONPATH=$(pwd):$PYTHONPATH
-export DATA_ROOT_DIR=${ONESCIENCE_DATASETS_DIR}/AlphaGeonme
-export MODEL_ROOT_DIR=${ONESCIENCE_MODELS_DIR}/AlphaGeonme
+export DATA_ROOT_DIR=${ONESCIENCE_DATASETS_DIR}/AlphaGenome
+export MODEL_ROOT_DIR=${ONESCIENCE_MODELS_DIR}/AlphaGenome
 
 python run_track_prediction_eval.py \
     --model_dir ${MODEL_ROOT_DIR}/alphagenome-all-folds \
     --model_version ALL_FOLDS \
+    --data_dir ${DATA_ROOT_DIR}/v1/train \
     --output_path ./outputs_track/eval_results.csv
 
diff --git a/examples/biosciences/alphagenome/run_variant.sh b/examples/biosciences/alphagenome/run_variant.sh
old mode 100644
new mode 100755
index 6e14478b458056bae590ba3cc65a1cd32475daa2..a494a6b597470e5c2a946eed642b978a6b88fe7a
--- a/examples/biosciences/alphagenome/run_variant.sh
+++ b/examples/biosciences/alphagenome/run_variant.sh
@@ -2,10 +2,10 @@
 
 source ../../../env.sh
 export PYTHONPATH=$(pwd):$PYTHONPATH
-export DATA_ROOT_DIR=${ONESCIENCE_DATASETS_DIR}/AlphaGeonme
-export MODEL_ROOT_DIR=${ONESCIENCE_MODELS_DIR}/AlphaGeonme
+export DATA_ROOT_DIR=${ONESCIENCE_DATASETS_DIR}/AlphaGenome
+export MODEL_ROOT_DIR=${ONESCIENCE_MODELS_DIR}/AlphaGenome
 
 python run_variant_scoring.py \
     --fasta_path ${DATA_ROOT_DIR}/reference/HOMO_SAPIENS/GRCh38.p13.genome.fa \
     --model_dir ${MODEL_ROOT_DIR}/alphagenome-all-folds \
-    --output_dir ./outputs_variant
\ No newline at end of file
+    --output_dir ./outputs_variant
diff --git a/install.sh b/install.sh
index 0ec8c1fb2d37bc72dce455c3a5392d006f535b5c..6cc6c172023372470ae3d3898fbab7f9ebdc1e20 100644
--- a/install.sh
+++ b/install.sh
@@ -67,7 +67,7 @@ BIO_WHEELS=(
     "https://download.sourcefind.cn:65024/file/4/jax/DAS1.7/jax_rocm60_pjrt-0.4.34+das.opt1.dtk25042-py3-none-manylinux2014_x86_64.whl"
     "https://download.sourcefind.cn:65024/file/4/jax/DAS1.7/jax_rocm60_plugin-0.4.34+das.opt1.dtk25042-cp311-cp311-manylinux2014_x86_64.whl"
     "https://download.sourcefind.cn:65024/file/4/jax/DAS1.7/jaxlib-0.4.34+das.opt1.dtk25042-cp311-cp311-manylinux2014_x86_64.whl"
-    "https://download.sourcefind.cn:65024/directlink/4/transformer_engine/DAS1.7/transformer_engine-2.7.0+das.opt1.dtk25042-cp311-cp311-manylinux_2_28_x86_64.whl"
+    "https://download.sourcefind.cn:65024/directlink/4/transformer_engine/DAS1.7/transformer_engine-2.5.0+das.opt1.dtk25042-cp311-cp311-manylinux_2_28_x86_64.whl"
     "https://download.sourcefind.cn:65024/directlink/4/flash_attn/DAS1.7/flash_attn-2.6.1+das.opt1.dtk25042-cp311-cp311-manylinux_2_28_x86_64.whl"
     "https://download.sourcefind.cn:65024/directlink/9/onesicence/dtk-25.04.2/bionemo_noodles-0.1.2-cp311-cp311-manylinux_2_28_x86_64.whl"
     "https://download.sourcefind.cn:65024/directlink/9/onesicence/dtk-25.04.2/nemo_toolkit-2.5.0rc0-py3-none-any.whl"
diff --git a/requirements.txt b/requirements.txt
index e9caa43634019b99627b7a6f67b5fcd453d91930..621cb06b21e9984a50ca66cce9c152e37424e7c2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -112,7 +112,7 @@ pwact
 
 #alphagenome
 alphagenome>=0.1.0
-kagglehub>=0.3.0
+kagglehub>=0.3.0,<=0.3.3
 orbax-checkpoint>=0.6.0
 pyfaidx>=0.7.0
 jaxtyping>=0.2.0
diff --git a/setup.py b/setup.py
index 8d32dfe9b5c5d85870fe1bb7b895c48658d8ccb6..bf1f75e3f186676d08d4cdf85c5fe66555929296 100644
--- a/setup.py
+++ b/setup.py
@@ -266,6 +266,7 @@ bio_requires = [
     "pytest",
     "pdbfixer",
     "e3nn",
+    "pyranges",
 ]
 
 matchem_requires = [
diff --git a/src/onescience/flax_models/alphagenome/package_config.py b/src/onescience/flax_models/alphagenome/package_config.py
new file mode 100644
index 0000000000000000000000000000000000000000..42784530caf7855afa24da76da2f34c0acb283db
--- /dev/null
+++ b/src/onescience/flax_models/alphagenome/package_config.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+"""
+AlphaGenome package config.
+
+Expose runtime metadata files through the normal packaging pipeline so
+install scripts do not need to copy files into site-packages manually.
+"""
+
+ALPHAGENOME_PACKAGE_DATA = {
+    "onescience.flax_models.alphagenome.model.metadata": [
+        "*.textproto",
+    ],
+}
+
+ALPHAGENOME_MANIFEST_RULES = [
+    "recursive-include src/onescience/flax_models/alphagenome/model/metadata *.textproto",
+]
+
+
+def get_package_data():
+    return ALPHAGENOME_PACKAGE_DATA
+
+
+def get_manifest_rules():
+    return ALPHAGENOME_MANIFEST_RULES