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chore: Migrate gsutil usage to gcloud storage #80

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d0dd6a5
chore: Migrate gsutil usage to gcloud storage
gurusai-voleti Feb 17, 2026
7cb3dfc
Update Inspecting_DeepConsensus_examples_and_running_model.ipynb
gurusai-voleti Feb 17, 2026
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8 changes: 4 additions & 4 deletions docs/generate_examples.md
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Expand Up @@ -58,14 +58,14 @@ mkdir "${TF_EXAMPLES_DIR}/eval"
mkdir "${TF_EXAMPLES_DIR}/test"

# Download the input PacBio Subread data.
gsutil cp gs://brain-genomics-public/research/deepconsensus/quickstart/v1.2/n1000.subreads.bam "${BASE_DIR}"/
gcloud storage cp gs://brain-genomics-public/research/deepconsensus/quickstart/v1.2/n1000.subreads.bam "${BASE_DIR}"/

# Truth Reference
gsutil cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/chm13v2.0_noY.fa "${BASE_DIR}"/
gcloud storage cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/chm13v2.0_noY.fa "${BASE_DIR}"/
# Truth exclude BED
gsutil cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/chm13v2.0_noY_hifi.issues.bed "${BASE_DIR}"/
gcloud storage cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/chm13v2.0_noY_hifi.issues.bed "${BASE_DIR}"/
# Truth split
gsutil cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/chm13v2.0_noY.chrom_mapping.txt "${BASE_DIR}"/
gcloud storage cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/chm13v2.0_noY.chrom_mapping.txt "${BASE_DIR}"/

cd "${BASE_DIR}"
```
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4 changes: 2 additions & 2 deletions docs/quick_start.md
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Expand Up @@ -112,10 +112,10 @@ QS_DIR="${HOME}/deepconsensus_quick_start"
mkdir -p "${QS_DIR}" "${QS_DIR}/model"

# Download the input PacBio Subread data.
gsutil cp gs://brain-genomics-public/research/deepconsensus/quickstart/v1.2/n1000.subreads.bam "${QS_DIR}"/
gcloud storage cp gs://brain-genomics-public/research/deepconsensus/quickstart/v1.2/n1000.subreads.bam "${QS_DIR}"/

# Download the DeepConsensus model.
gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* "${QS_DIR}"/model/
gcloud storage cp --recursive gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* "${QS_DIR}"/model/
```

This directory should now contain the following files:
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2 changes: 1 addition & 1 deletion docs/train_model.md
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Expand Up @@ -43,7 +43,7 @@ mkdir "${DC_TRAIN_DIR}"
mkdir "${TF_EXAMPLES}"
mkdir "${DC_TRAIN_OUTPUT}"

gsutil -m cp -R gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/* "${TF_EXAMPLES}/"
gcloud storage cp --recursive gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/* "${TF_EXAMPLES}/"
```

The path to training examples has to be set in
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2 changes: 1 addition & 1 deletion docs/train_tpu_model.md
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Expand Up @@ -260,7 +260,7 @@ Copy DeepConsensus checkpoint locally:

```bash
mkdir /mnt/disks/persist/model_checkpoint
gsutil cp gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* /mnt/disks/persist/model_checkpoint/
gcloud storage cp gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* /mnt/disks/persist/model_checkpoint/
```

Add optional `--checkpoint` flag to
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5 changes: 2 additions & 3 deletions notebooks/Inspecting_DeepConsensus_examples_and_running_model.ipynb
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Expand Up @@ -383,10 +383,9 @@
"source": [
"# Download Model\n",
"! mkdir -p deepconsensus_model\n",
"! gsutil cp -r gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* deepconsensus_model/\n",
"! gcloud storage cp --recursive gs://brain-genomics-public/research/deepconsensus/models/v1.2/model_checkpoint/* deepconsensus_model/\n",
"# Download test data\n",
"! gsutil cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/test/tf-test-00000-of-00500.tfrecord.gz ./tf-test.tfrecord.gz"
]
"! gcloud storage cp gs://brain-genomics-public/research/deepconsensus/training-tutorial/v1.2/test/tf-test-00000-of-00500.tfrecord.gz ./tf-test.tfrecord.gz" ]
},
{
"cell_type": "code",
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