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chore: Migrate gsutil usage to gcloud storage #83

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10 changes: 5 additions & 5 deletions docs/deepsomatic-hybrid-pacbio-illumina.md
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Expand Up @@ -40,21 +40,21 @@ mkdir -p "${OUTPUT_DIR}"
mkdir -p "${OUTPUT_DIR}/sompy_output"

# Download PacBio Tumor Bam
gsutil cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395.GRCh38.tumor.chr1.nygc.bam* ${INPUT_DIR}/
gcloud storage cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395.GRCh38.tumor.chr1.nygc.bam* ${INPUT_DIR}/

# Download Illumina Normal WGS
gsutil cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395_wgs.normal.chr1.bam* ${INPUT_DIR}/
gcloud storage cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/HCC1395_wgs.normal.chr1.bam* ${INPUT_DIR}/

# Download a reference genome
gsutil cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna* ${INPUT_DIR}/
gcloud storage cp gs://deepvariant/deepsomatic-case-studies/deepsomatic-chr1-case-studies/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr1.fna* ${INPUT_DIR}/

# Download truth VCF
gsutil -m cp gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/High-Confidence_Regions_v1.2.bed \
gcloud storage cp gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/High-Confidence_Regions_v1.2.bed \
gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/high-confidence_sINDEL_sSNV_in_HC_regions_v1.2.1.merged.vcf.gz* \
gs://deepvariant/deepsomatic-case-studies/SEQC2-S1395-truth/seqc2_hg38.exome_regions.bed ${INPUT_DIR}

# Download the model
gsutil -m cp gs://deepvariant/models/experimental/deepsomatic_hybrid/exp_157994267/* ${INPUT_DIR}
gcloud storage cp gs://deepvariant/models/experimental/deepsomatic_hybrid/exp_157994267/* ${INPUT_DIR}
```

## Running DeepSomatic with one command
Expand Down